This audit records the editions available on 12 October 2026. The 7 November revisions to the nuclear speckles and merged chromatin web reviews have a separate release date.
85 HTML reviews previously appraised; 23 Downloads-linked topics now completely rewritten in matching Word and webpage editions. This covers the prior 68 research pages/guides and 17 hypothesis reviews; three supplemental pages also retain their source appraisals.
Scientific citations are primary experimental, observational, mathematical or method studies and selected seminal reviews. Correction notices accompany affected primary papers as publication provenance.
The current ledger contains 664 per-review reference appraisals. Its hashes and source records for the 23 rewritten pages describe the new editions. Earlier records below for other pages retain their recorded access depth. Scientific source fit, static checks, document rendering and experimental replication are distinct stages.
Original Word drafts, complete supplements, raw data and individual image provenance are outside this current-edition appraisal. Notice searches are incomplete for some recent papers. A missing indexed notice does not establish that no notice exists.
Examples of claims checked directly
Feric's tracer measurements use 50 nm-radius particles in reconstituted protein droplets. They are distinct from whole-nucleus viscosity and the in-vivo viscosity-to-surface-tension ratio. Primary study.
The reported 10–30 minute loop lifetime is a model-inferred median at the Fbn2 locus in a defined mouse embryonic stem-cell context. Primary study.
Routh's fiber widths describe H5-saturated reconstituted nucleosome arrays examined by negative-stain EM; the stated variation is standard deviation. Primary study.
Recent MINFLUX results support selected fiber-like localization patterns, with dye, sampling and topology limits stated beside the findings. Primary study, online 2025 and 2026 issue.
SC35's historical label is distinguished from the SRRM2 antibody-target result; unverified archive reagents are not reassigned. Primary study.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (7)
10.1073/pnas.0601212103 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1073/pnas.0802336105 — primary research. Access: selected primary body plus root browser results figure3 methods. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected body inspected. Root independently opened actualPMC2440727 Results/Figure3 and negative-stainMethods, confirming 167bpNRL21.3nmSD3.0 and197bpNRL34.3nmSD2.7; 99measurements each. No native-cell generalization.
10.1038/emboj.2012.35 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1126/science.aag0025 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41467-023-42072-1 — primary research. Access: selected primary body and indexed results methods. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite first body page and official indexed primary Results/Discussion/Methods support frozen CEM periphery, variable20–50nm arrangements, relaxed zigzags and partial linker/H1 resolution. PrimaryTable1 and classificationMethods confirm5tomograms and6790selectedparticles. Sampling limits retained.
10.1038/s41467-026-75087-5 — primary research. Access: primary publisher results and methods. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Official publisher article published3July2026 volume17article5844. Results, reconstruction limitations and main Methods inspected; 2026 retained despite Consensus record indexing2025.
MINFLUX dissects nucleosome and compacting chromatin structures in living cells — primary method and experiment. Access: Scite primary body: Introduction, Results and Discussion inspected; supplementary data and raw localizations not reanalyzed.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Scientific text and references appraised at recorded source depth · hypothesis
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Dynamics of microcompartment formation at the mitosis-to-G1 transition — primary experimental and computational research. Access: Consensus fetched primary abstract; Scite main body introduction/Results context. Claim fit: Mouse erythroid RCMC microcompartments and polymer model; contact microcompartments partly distinct from A/B compartments
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Falk publisher correction content remains subscription-restricted; no numerical claim depends on its uninspected content.
Scientific text and references appraised at recorded source depth · hypothesis
A recent RNA-processing perturbation tests architectural causation
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (4)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary study. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.
Phase transitions in the assembly of multivalent signalling proteins — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Multivalent demixing with qualified sol–gel interpretation in reconstituted mixtures; not universal nuclear percolation threshold.
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Quinodoz and colleagues spatially mapped rRNA maturation and engineered nucleoli with processing defects. Disrupting small-subunit processing reordered nucleolar layers and blocked normal rRNA outflux. This provides a substrate-linked perturbation of multiphase architecture, complementary to earlier material measurements. It does not establish that every nuclear body contains a permanent solid core or that all RNA-protein assemblies use the same phase mechanism. Quinodoz et al. (2025) .
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (4)
10.1126/science.1186777 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1126/science.abn6583 — primary research. Access: selected primary body plus root browser results figure3. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected body inspected. Root independently opened actualPMC9069445 ResultsP14/P15 and Figure3D-F, confirming model-inferred median10–30min with censoring correction, distinct mean15–45min; one505kbFbn2G1/earlyS mESCcontext.
10.1371/journal.pone.0010531 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
Uniform dynamics of cohesin-mediated loop extrusion in living human cells — primary experiment and model. Access: Consensus fetched primary abstract and Scite selected main-text passages, including study design and initial Results; not every supplementary analysis inspected.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (5)
10.1016/j.cell.2019.08.037 — primary research. Access: indexed primary results discussion plus root browser results figures2 5 7. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite provided Highlights; Consensus fetch supplied only a takeaway, which was not used as evidence. Indexed primary PMC Results/Discussion inspected. Root independently opened actualPMC6778041 ResultsP18+Fig2whole/partialFRAP, P32+Fig5p300/AcetylCoA recruitment-dependent dissolution, and P39+Fig7acetylchromatin/reader multivalency. MainResults and captions support retained fusion/exchange/acetylation/reader observations; supplements/rawdata not reanalyzed.
10.1016/j.molcel.2020.02.005 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/emboj.2012.35 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1126/science.aao6135 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
HP1 loses its chromatin clustering and phase separation function across evolution — primary experiment. Access: Consensus fetched primary abstract and official publisher abstract and selected Results inspected. Scite had metadata but no readable body.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (3)
10.1371/journal.pbio.0030157 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/nature08973 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
Cell type–specific 3D-genome organization and transcription regulation in the brain — primary imaging and perturbation. Access: Consensus fetched primary abstract and Scite selected Introduction and initial Results inspected, including combined DNA/RNA-MERFISH in mouse primary motor cortex.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
10.1038/s41467-023-39846-y — primary research. Access: selected primary body and indexed results. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected primarybody inspected; indexedPMC10333366Results independently confirm H1e/H3K27me3regional associations, partialH1c/d/e-loss with unchangedSUZ12, restoration/mark/mRNA distinctions. Full supplementalmechanistic validation not reproduced.
10.1016/j.molcel.2020.02.005 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
The fork protection complex promotes parental histone recycling and epigenetic memory — primary experiment. Access: Consensus fetched primary abstract; Scite Introduction, main-text study summary, Figure 1 caption and initial Results inspected. Supplementary validation and raw data not reanalyzed.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Scientific text and references appraised at recorded source depth · hypothesis
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (3)
Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose) — primary experimental research. Access: Scite identity; actual official Nature Communications primary main Results/Fig1–5 captions. Claim fit: PAR-dependent FET recruitment and RGG/domain comparisons in U-2-OS; endogenous recruitment distinct from ectopic domain droplets
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (6)
10.1016/j.celrep.2016.04.085 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1016/j.cell.2017.09.026 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41586-023-05961-5 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1126/science.abn6583 — primary research. Access: selected primary body plus root browser results figure3. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected body inspected. Root independently opened actualPMC9069445 ResultsP14/P15 and Figure3D-F, confirming model-inferred median10–30min with censoring correction, distinct mean15–45min; one505kbFbn2G1/earlyS mESCcontext.
10.1038/s41588-022-01223-8 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
Uniform dynamics of cohesin-mediated loop extrusion in living human cells — primary experiment and model. Access: Consensus fetched primary abstract and Scite selected main-text passages, including study design and initial Results; not every supplementary analysis inspected.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Scientific text and references appraised at recorded source depth · hypothesis
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (5)
Compositional Control of Phase-Separated Cellular Bodies — primary experimental research. Access: Scite primary abstract; actual PMC4967043 main Results, scaffold/client comparisons, Fig1–5 descriptions. Claim fit: Specific client binding, scaffold stoichiometry/valency, selective partitioning and different component recovery; model systems do not diagnose all bodies
Phase transitions in the assembly of multivalent signalling proteins — primary experimental research. Access: Scite primary Methods summary and figure captions plus qualified discussion excerpt; abstract identity. Claim fit: SH3/PRM, PTB/RNA and nephrin systems; valency-dependent demixing and qualified sol–gel coupling; no universal endogenous phase diagnosis
Determinants that enable disordered protein assembly into discrete condensed phases — primary experimental research. Access: Scite identity; official publisher/PubMed primary abstract; detailed body denied. Claim fit: Selective IDR co-assembly, purified mixtures, modeling and mutations; system-specific detail narrowed to available source depth
A single cluster of RNA Polymerase II molecules is stably associated with active genes — primary experimental research. Access: Consensus fetched record + Scite primary abstract; official publisher main Results/Discussion read. Claim fit: Fly-embryo Pol II clustering explained by engaged-polymerase accumulation with imaging and simulations; ordinary clusters distinct from histone locus bodies; publisher date resolves Consensus 2025 metadata discrepancy
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Scientific text and references appraised at recorded source depth · hypothesis
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (7)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary experimental research. Access: Scite primary abstract; root independently read actual PMC5127388 main Results, Fig2E and main Methods on 12 October; supplements not read. Claim fit: Xenopus nucleoli plus NPM1/FIB1/RNA reconstitution, two reconstituted condensed phases and solution, component differences; R=50-nm probe particles in vitro, in-vivo fusion constrains viscosity/surface-tension ratio
Compositional Control of Phase-Separated Cellular Bodies — primary experimental research. Access: Scite primary abstract; actual PMC4967043 main Results, scaffold/client comparisons, Fig1–5 descriptions. Claim fit: Specific client binding, scaffold stoichiometry/valency, selective partitioning and different component recovery; model systems do not diagnose all bodies
Phase transitions in the assembly of multivalent signalling proteins — primary experimental research. Access: Scite primary Methods summary and figure captions plus qualified discussion excerpt; abstract identity. Claim fit: SH3/PRM, PTB/RNA and nephrin systems; valency-dependent demixing and qualified sol–gel coupling; no universal endogenous phase diagnosis
Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins — primary experimental research. Access: Scite identity; SciSpace primary abstract; root actual PMC3998805 main Results and Fig2/Fig3 captions. Claim fit: Oxidative PML mesh, subsequent SUMO/SIM partner retention, partner SUMOylation and selected RNF4 degradation; narrow CHO shell/core immuno-EM in Fig3B retained
1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells — primary experimental research. Access: Scite primary main body introduction and indexed primary result context. Claim fit: Human cell-line chromatin motion/compaction effects make hexanediol sensitivity a nonselective phase-mechanism test
Dynamic interaction of spliceosomal snRNPs with coilin explains Cajal body characteristics — primary experimental research. Access: SciSpace primary abstract; Scite primary main body opening plus targeted Results/Discussion excerpts. Claim fit: Coilin/snRNP interaction and RNA-dependent oligomerization, coilin boundary constraint; single-component LLPS model insufficient
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Scientific text and references appraised at recorded source depth · hypothesis
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (6)
Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins — primary experimental research. Access: Scite identity; SciSpace primary abstract; root actual PMC3998805 main Results and Fig2/Fig3 captions. Claim fit: Oxidative PML mesh, subsequent SUMO/SIM partner retention, partner SUMOylation and selected RNF4 degradation; narrow CHO shell/core immuno-EM in Fig3B retained
1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells — primary experimental research. Access: Scite primary main body introduction and indexed primary result context. Claim fit: Human cell-line chromatin motion/compaction effects make hexanediol sensitivity a nonselective phase-mechanism test
Mediator and RNA polymerase II clusters associate in transcription-dependent condensates — primary experimental research. Access: Scite indexed primary figure captions and targeted excerpts; recorded body text only 4,760 characters, not full original main article. Claim fit: mESC endogenous clusters, JQ1/DRB dependencies, six-cell Esrrb proximity, recovery/merging; exchange and proximity not uniquely a phase mechanism
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
10.1038/s41467-023-39846-y — primary research. Access: selected primary body and indexed results. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected primarybody inspected; indexedPMC10333366Results independently confirm H1e/H3K27me3regional associations, partialH1c/d/e-loss with unchangedSUZ12, restoration/mark/mRNA distinctions. Full supplementalmechanistic validation not reproduced.
The fork protection complex promotes parental histone recycling and epigenetic memory — primary experiment. Access: Consensus fetched primary abstract; Scite Introduction, main-text study summary, Figure 1 caption and initial Results inspected. Supplementary validation and raw data not reanalyzed.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Scientific text and references appraised at recorded source depth · hypothesis
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice — primary experimental research. Access: Scite short primary abstract; official PubMed primary abstract. Claim fit: Mouse tissue-selective NEAT1_2/paraspeckles and viable/fertile deficient animals under reported conditions; no universal human physiology conclusion
Paraspeckles are constructed as block copolymer micelles — primary experimental and theoretical research. Access: Scite primary abstract. Claim fit: RNA-domain deletion/transcription comparisons plus explicitly proposed micellization model
Paraspeckle condensation is controlled via TDP-43 polymerization and linked to neuroprotection — primary experimental research. Access: Consensus fetched primary abstract; Scite primary main Results beginning. Claim fit: Concentration/polymerization/RNA-binding-dependent paraspeckle regulation; repeat deletion and stressed human-neuron cytoprotection, patient survival association not clinical efficacy
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (4)
10.1126/science.1181369 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41586-019-1778-y — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1126/science.abn6583 — primary research. Access: selected primary body plus root browser results figure3. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected body inspected. Root independently opened actualPMC9069445 ResultsP14/P15 and Figure3D-F, confirming model-inferred median10–30min with censoring correction, distinct mean15–45min; one505kbFbn2G1/earlyS mESCcontext.
Uniform dynamics of cohesin-mediated loop extrusion in living human cells — primary experiment and model. Access: Consensus fetched primary abstract and Scite selected main-text passages, including study design and initial Results; not every supplementary analysis inspected.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Scientific text and references appraised at recorded source depth · research
RNA transport inside a nucleolus differs from reporter diffusion
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (6)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary study. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Quinodoz and colleagues combined sequencing with imaging to map spatially separated rRNA processing stages. In engineered nucleoli, disrupting small-subunit processing altered layer order and impeded outward rRNA movement. This is substrate-processing-associated motion within a particular body; it should not be assigned the diffusion coefficients of inert eGFP probes or treated as transport across the nuclear envelope. Quinodoz et al. (2025) .
Simple rules for passive diffusion through the nuclear pore complex — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.
Mapping eGFP Oligomer Mobility in Living Cell Nuclei — primary study. Access: Primary PLOS main Abstract, Methods data analysis/acquisition/calibration and selected Results/Discussion; no raw data reanalysis.. Claim fit: eGFP oligomer FCS outside nucleoli: calibrated two-normal-diffusion components plus triplet term; cell/model/probe constraints retained.
Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Reaction-diffusion FRAP solutions constrain binding inference; not every recovery curve identifies every parameter.
Robust model-based analysis of single-particle tracking experiments with Spot-On — primary study. Access: Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.. Claim fit: Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Rao 2014 erratum identified and explicitly linked; qualitative claim retained without uncorrected orientation counts.
Sources and access depth (7)
10.1126/science.aag0025 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41467-023-42072-1 — primary research. Access: selected primary body and indexed results methods. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite first body page and official indexed primary Results/Discussion/Methods support frozen CEM periphery, variable20–50nm arrangements, relaxed zigzags and partial linker/H1 resolution. PrimaryTable1 and classificationMethods confirm5tomograms and6790selectedparticles. Sampling limits retained.
10.1038/s41467-026-75087-5 — primary research. Access: primary publisher results and methods. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Official publisher article published3July2026 volume17article5844. Results, reconstruction limitations and main Methods inspected; 2026 retained despite Consensus record indexing2025.
10.1016/j.cell.2014.11.021 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1126/science.aau1783 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1126/science.abn6583 — primary research. Access: selected primary body plus root browser results figure3. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected body inspected. Root independently opened actualPMC9069445 ResultsP14/P15 and Figure3D-F, confirming model-inferred median10–30min with censoring correction, distinct mean15–45min; one505kbFbn2G1/earlyS mESCcontext.
MINFLUX dissects nucleosome and compacting chromatin structures in living cells — primary method and experiment. Access: Scite primary body: Introduction, Results and Discussion inspected; supplementary data and raw localizations not reanalyzed.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
This narrative integrates foundational and recent primary studies available by 12 October 2026. Source access ranges from original abstracts to selected Results, figure captions and Methods, as specified for each reference. It is a scholarly synthesis of the measured systems; it does not independently reproduce their experiments, analyze their raw data or establish exhaustive literature coverage.
Sources and access depth (22)
Reconstitution of mitotic chromatids with a minimum set of purified factors — primary. Access: Original PubMed abstract and SciSpace indexed primary abstract inspected.. Claim fit: Six-factor reconstitution, embryonic H2A.X-F/FACT substrate dependence and condensin-I Cdk1 phosphorylation; sufficiency in the defined preparation.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Real-time imaging of DNA loop extrusion by condensin — primary. Access: Consensus search and fetched original abstract inspected in this rewrite.. Claim fit: Direct purified yeast-condensin loop extrusion on DNA; ATP dependence, asymmetry and force-dependent behavior.. Limits: Purified DNA assay; cellular loop paths and complete chromosome assembly not directly observed.
A pathway for mitotic chromosome formation — primary. Access: Prior audit selected original Results and Figures 1–5; reference ledger and source-linked narrative re-read for this rewrite.. Claim fit: Synchronized DT40 mitotic Hi-C, condensin depletion and hierarchical loop-model interpretation.. Limits: Population contacts and polymer-model fit; supplements and raw contact data not reanalyzed.
A quantitative map of human Condensins provides new insights into mitotic chromosome architecture — primary. Access: Prior audit original main Results, captions and Discussion; ledger and narrative re-read.. Claim fit: HeLa Kyoto endogenous condensin numbers, axial localization and mitotic association dynamics; loop paths remain hypothetical.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Rules of engagement for condensins and cohesins guide mitotic chromosome formation — primary. Access: Prior audit fetched Consensus original abstract and selected original main Results; source ledger re-read.. Claim fit: DT40 condensin/cohesin engagement, compaction versus rod individualization, and integrated model interpretation.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Crystal structure of the nucleosome core particle at 2.8 Å resolution — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Histone octamer, DNA superhelix and histone-tail contacts in the crystallized nucleosome.. Limits: Crystallized core particle; not a direct measurement of chromatin dynamics or whole-nucleus packing.
Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Chicken erythrocyte fiber stretch/release, ionic-strength dependence and irreversible high-force changes.. Limits: Isolated specialized chromatin; fitted persistence length and force transitions not universal nuclear constants.
Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure — primary. Access: Prior audit original Results, Figure 3 and negative-stain Methods; source ledger re-read.. Claim fit: Reconstituted 167/197-bp repeat arrays, H5-dependent compaction and geometry.. Limits: Artificial arrays and negative-stain EM; no direct living-cell fiber census.
Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Chemically defined H4K16-acetylated arrays inhibit folding and cross-fiber interactions and alter ACF remodeling.. Limits: Defined in-vitro substrate; not evidence that all acetylation effects in cells are direct fiber unfolding.
Organization of Chromatin by Intrinsic and Regulated Phase Separation — primary. Access: Prior audit original Results/Discussion and browser Figures 2, 5 and 7; ledger re-read.. Claim fit: Nucleosome-array droplet reconstitution, salt/concentration dependence, H1 and acetylation effects; internal versus whole-droplet recovery.. Limits: Purified arrays under stated conditions; a cellular phase mechanism is not inferred for all chromatin.
Structure of native chromatin fibres revealed by Cryo-ET in situ — primary. Access: Prior audit original selected Results and Methods; ledger re-read.. Claim fit: Cryo-ET in interphase CEM cells reveals heterogeneous local zigzag organization near the envelope.. Limits: Limited cryogenic volumes and cellular model; local arrangements do not define a genome-wide polymer conformation.
Molecular architecture of heterochromatin at the nuclear periphery of primary human cells — primary. Access: Prior audit original publisher Results and Methods; ledger re-read.. Claim fit: Resting primary human CD4+ T-cell peripheral chromatin, heterogeneous elongated arrangement and frequent nucleosome stacking.. Limits: Selected cellular region and quiescent state; observed envelope width is not proof of canonical fiber periodicity.
MINFLUX dissects nucleosome and compacting chromatin structures in living cells — primary. Access: Prior audit indexed original Introduction, Results and Discussion; ledger re-read.. Claim fit: DNA-probe MINFLUX localizations, selected living-U2OS fiber-like domains and probe/sampling limits.. Limits: AT-preferring probe, selected trajectories and possible probe stabilization; localization precision differs from structural resolution.
Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging — primary. Access: Prior audit original selected Results and browser Figure 3; ledger re-read.. Claim fit: Fbn2 distances, protein perturbations and Bayesian/censoring-corrected estimates of looped states.. Limits: One silent 505-kb locus in mESC G1/early S; model-inferred state and lifetime, not direct extrusion movies.
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization — primary. Access: Prior audit selected original model Results and Methods; ledger re-read.. Claim fit: Brownian bead-spring polymer with reversible multivalent bridging can form clusters without direct protein attraction.. Limits: Coarse-grained equilibrium model; not proof that a specific nuclear assembly is produced by bridging.
HP1 loses its chromatin clustering and phase separation function across evolution — primary. Access: Original publisher abstract and main Results on homolog comparison, phase diagrams and cellular coalescence inspected in this rewrite; earlier audit also read selected Results.. Claim fit: Side-by-side Swi6, fly HP1a and mouse HP1α comparisons, paralog antagonism and heterologous fibroblast tests.. Limits: GFP fusion/reconstitution and heterologous-expression contexts; not a census of all tissues or all HP1 functions.
Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus — primary. Access: Independent biophysics agent original abstract and verified DOI/title metadata; source ledger read in this rewrite.. Claim fit: Isolated-nucleus small-extension chromatin versus larger-extension lamin-A-dependent response regimes.. Limits: Isolated imposed-extension geometry; no universal chromatin modulus or nuclear viscosity.
Heterogeneous force response of chromatin in isolated nuclei — primary. Access: Independent biophysics agent fetched original Consensus abstract and SciSpace cross-check; evidence metadata read.. Claim fit: Joint imposed-force, chromatin and envelope-deformation measurements in isolated nuclei.. Limits: Abstract-bounded; prepared nuclei and strain regime, not every live-cell mechanical context.
Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response — primary. Access: Independent biophysics agent fetched original abstract and indexed method/measurement comparisons; evidence metadata read.. Claim fit: Polymer/tether model constrained by mechanical and chromosome-contact observations; modeled peripheral coupling controls force transmission.. Limits: Model-supported account, not direct identification of every native molecular tether.
This narrative integrates foundational and recent primary studies available by 12 October 2026. Source access ranges from original abstracts to selected Results, figure captions and Methods, as specified for each reference. It is a scholarly synthesis of the measured systems; it does not independently reproduce their experiments, analyze their raw data or establish exhaustive literature coverage.
Sources and access depth (19)
Crystal structure of the nucleosome core particle at 2.8 Å resolution — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Histone octamer, DNA superhelix and histone-tail contacts in the crystallized nucleosome.. Limits: Crystallized core particle; not a direct measurement of chromatin dynamics or whole-nucleus packing.
Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure — primary. Access: Prior audit original Results, Figure 3 and negative-stain Methods; source ledger re-read.. Claim fit: Reconstituted 167/197-bp repeat arrays, H5-dependent compaction and geometry.. Limits: Artificial arrays and negative-stain EM; no direct living-cell fiber census.
Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Chemically defined H4K16-acetylated arrays inhibit folding and cross-fiber interactions and alter ACF remodeling.. Limits: Defined in-vitro substrate; not evidence that all acetylation effects in cells are direct fiber unfolding.
Structure of native chromatin fibres revealed by Cryo-ET in situ — primary. Access: Prior audit original selected Results and Methods; ledger re-read.. Claim fit: Cryo-ET in interphase CEM cells reveals heterogeneous local zigzag organization near the envelope.. Limits: Limited cryogenic volumes and cellular model; local arrangements do not define a genome-wide polymer conformation.
Molecular architecture of heterochromatin at the nuclear periphery of primary human cells — primary. Access: Prior audit original publisher Results and Methods; ledger re-read.. Claim fit: Resting primary human CD4+ T-cell peripheral chromatin, heterogeneous elongated arrangement and frequent nucleosome stacking.. Limits: Selected cellular region and quiescent state; observed envelope width is not proof of canonical fiber periodicity.
Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging — primary. Access: Prior audit original selected Results and browser Figure 3; ledger re-read.. Claim fit: Fbn2 distances, protein perturbations and Bayesian/censoring-corrected estimates of looped states.. Limits: One silent 505-kb locus in mESC G1/early S; model-inferred state and lifetime, not direct extrusion movies.
Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells — primary. Access: Consensus search and fetched original abstract inspected; publisher body access failed.. Claim fit: Acute H3K9 methyltransferase depletion in engineered mESCs, heterogeneous mark decay and HP1 threshold-associated opening.. Limits: Abstract-bounded; four stability classes in this engineered pluripotent-cell context, not universal decay constants.
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping — primary. Access: Prior audit original abstract plus selected indexed results; associated erratum checked.. Claim fit: Population contact compartments, histone/accessibility associations and loop organization.. Limits: Population contacts; GM12878 peak-file erratum affects detailed motif statistics, which are not used in this rewrite.
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells — primary. Access: Prior audit original abstract; ledger re-read.. Claim fit: Selected chromosome-21 fixed-cell intervals; variable domain boundaries and cohesin-depleted HCT116 comparisons.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Histone modifications at human enhancers reflect global cell-type-specific gene expression — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Multi-cell-type chromatin maps and enhancer activity associate enhancer signatures with cell-specific expression programs.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming — primary. Access: Original abstract in Consensus search read; fetched record confirms identity but contains takeaway only.. Claim fit: Purified Oct4, Sox2 and Klf4 nucleosome binding and cellular targeting of nucleosome-enriched silent sites.. Limits: Full Results not appraised; c-Myc must not be grouped with the three factors as an equally demonstrated nucleosome-binding pioneer.
SWI/SNF-dependent genes are defined by their chromatin landscape — primary. Access: Prior audit fetched original Consensus abstract; identity checked against indexed DOI metadata.. Claim fit: Chromatin landscape association with gene-specific SWI/SNF dependence; claims restricted to original abstract.. Limits: No complete original main Results or supplementary analysis inspected.
Two distinct modes for propagation of histone PTMs across the cell cycle — primary. Access: Prior audit original main Results, Figures 1–4 and Discussion; ledger re-read.. Claim fit: Nascent-chromatin isotope/mass-spectrometry study distinguishes parental and new histone modification kinetics.. Limits: Population peptides, not genomic address or every pair of modifications on one nucleosome; supplementary cell-line details not appraised.
Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction — primary. Access: Prior audit original selected Results and Discussion; ledger re-read.. Claim fit: mESC H1c/d/e-depleted comparison, chromatin compaction and delayed H3K27me3 restoration on replicated DNA.. Limits: Ensemble occupancy and fitted restoration rates; chronic depletion may have indirect effects.
The fork protection complex promotes parental histone recycling and epigenetic memory — primary. Access: Prior audit fetched original abstract and selected main Results/Figure 1; ledger re-read.. Claim fit: Fork-protection-complex contribution to parental histone recycling and epigenetic-memory maintenance.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
This narrative integrates foundational and recent primary studies available by 12 October 2026. Source access ranges from original abstracts to selected Results, figure captions and Methods, as specified for each reference. It is a scholarly synthesis of the measured systems; it does not independently reproduce their experiments, analyze their raw data or establish exhaustive literature coverage.
Sources and access depth (17)
Organization of Chromatin by Intrinsic and Regulated Phase Separation — primary. Access: Prior audit original Results/Discussion and browser Figures 2, 5 and 7; ledger re-read.. Claim fit: Nucleosome-array droplet reconstitution, salt/concentration dependence, H1 and acetylation effects; internal versus whole-droplet recovery.. Limits: Purified arrays under stated conditions; a cellular phase mechanism is not inferred for all chromatin.
Structure of native chromatin fibres revealed by Cryo-ET in situ — primary. Access: Prior audit original selected Results and Methods; ledger re-read.. Claim fit: Cryo-ET in interphase CEM cells reveals heterogeneous local zigzag organization near the envelope.. Limits: Limited cryogenic volumes and cellular model; local arrangements do not define a genome-wide polymer conformation.
Molecular architecture of heterochromatin at the nuclear periphery of primary human cells — primary. Access: Prior audit original publisher Results and Methods; ledger re-read.. Claim fit: Resting primary human CD4+ T-cell peripheral chromatin, heterogeneous elongated arrangement and frequent nucleosome stacking.. Limits: Selected cellular region and quiescent state; observed envelope width is not proof of canonical fiber periodicity.
MINFLUX dissects nucleosome and compacting chromatin structures in living cells — primary. Access: Prior audit indexed original Introduction, Results and Discussion; ledger re-read.. Claim fit: DNA-probe MINFLUX localizations, selected living-U2OS fiber-like domains and probe/sampling limits.. Limits: AT-preferring probe, selected trajectories and possible probe stabilization; localization precision differs from structural resolution.
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization — primary. Access: Prior audit selected original model Results and Methods; ledger re-read.. Claim fit: Brownian bead-spring polymer with reversible multivalent bridging can form clusters without direct protein attraction.. Limits: Coarse-grained equilibrium model; not proof that a specific nuclear assembly is produced by bridging.
Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin — primary. Access: Prior audit original abstract and selected Methods; ledger re-read.. Claim fit: Purified human HP1α, DNA, phosphorylation and partner partitioning demonstrate context-dependent droplet capacity.. Limits: In-vitro capacity is distinguished from a general mammalian cellular mechanism.
Phase separation drives heterochromatin domain formation — primary. Access: Prior audit original abstract; source narrative and ledger re-read.. Claim fit: Drosophila HP1a reconstitution and early embryonic liquid-like heterochromatin observations.. Limits: Early fly developmental context; detailed quantitative Methods not reappraised.
HP1 loses its chromatin clustering and phase separation function across evolution — primary. Access: Original publisher abstract and main Results on homolog comparison, phase diagrams and cellular coalescence inspected in this rewrite; earlier audit also read selected Results.. Claim fit: Side-by-side Swi6, fly HP1a and mouse HP1α comparisons, paralog antagonism and heterologous fibroblast tests.. Limits: GFP fusion/reconstitution and heterologous-expression contexts; not a census of all tissues or all HP1 functions.
Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins — primary. Access: Consensus fetched original abstract inspected.. Claim fit: HP1 chromodomain recognition of H3K9 methylation; Suv39h-double-null primary mouse fibroblast localization and catalytic rescue.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Specific methyl-lysine recognition and chromodomain-mutant comparisons; fission-yeast silencing context.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Role of the polycomb protein Eed in the propagation of repressive histone marks — primary. Access: Consensus fetched original abstract inspected.. Claim fit: EED recognition of repressive trimethyl-lysine marks and allosteric PRC2 activation; biochemical and fly-mutant evidence.. Limits: Reader–writer propagation model; does not alone prove a complete cellular inheritance mechanism.
Ten principles of heterochromatin formation and function — seminal review. Access: Consensus fetched review abstract and original publisher Key Points inspected.. Claim fit: Foundational distinctions among nucleation, spreading, maintenance, repetitive-DNA functions and lineage restriction.. Limits: Conceptual definitions supported by the seminal review; particular contemporary mechanisms cited to primary work.
Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells — primary. Access: Consensus search and fetched original abstract inspected; publisher body access failed.. Claim fit: Acute H3K9 methyltransferase depletion in engineered mESCs, heterogeneous mark decay and HP1 threshold-associated opening.. Limits: Abstract-bounded; four stability classes in this engineered pluripotent-cell context, not universal decay constants.
Two distinct modes for propagation of histone PTMs across the cell cycle — primary. Access: Prior audit original main Results, Figures 1–4 and Discussion; ledger re-read.. Claim fit: Nascent-chromatin isotope/mass-spectrometry study distinguishes parental and new histone modification kinetics.. Limits: Population peptides, not genomic address or every pair of modifications on one nucleosome; supplementary cell-line details not appraised.
Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction — primary. Access: Prior audit original selected Results and Discussion; ledger re-read.. Claim fit: mESC H1c/d/e-depleted comparison, chromatin compaction and delayed H3K27me3 restoration on replicated DNA.. Limits: Ensemble occupancy and fitted restoration rates; chronic depletion may have indirect effects.
The fork protection complex promotes parental histone recycling and epigenetic memory — primary. Access: Prior audit fetched original abstract and selected main Results/Figure 1; ledger re-read.. Claim fit: Fork-protection-complex contribution to parental histone recycling and epigenetic-memory maintenance.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
XRCC1 prevents toxic PARP1 trapping during DNA base excision repair — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: XRCC1-associated complexes limit detrimental PARP1 trapping at BER intermediates in deficient models; not universal PARP dispensability.
XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Lin and colleagues found that XRCC1 supported PARP1- and PAR-dependent recruitment of PARP2 to damaged regions. XRCC1 deficiency increased PARP1 activation while reducing micro-irradiation-associated PARP2 foci. This extends the scaffold question to ordered recruitment of two damage sensors; it does not establish that every BER intermediate or glycosylase uses the same hierarchy. Lin et al. (2025) .
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
This scholarly synthesis integrates foundational studies and literature available by 12 October 2026. Source access ranges from primary abstracts to selected Results, figure captions and Methods, as specified for each reference. Experiments and models retain their organism, construct and perturbation context; raw data and supplementary material have not been comprehensively reanalysed.
Coilin-dependent snRNP assembly is essential for zebrafish embryogenesis — primary. Access: Publisher primary abstract, Fig1–7 descriptions and 4 April 2010 inline correction notice. Claim fit: Coilin depletion, developmental and spliced-RNA deficits, rescue by assembled human snRNPs.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies — primary. Access: Primary publication abstract and bibliographic record. Claim fit: FRAP-constrained reaction model predicts assembly enhancement and tested SART3–coilin interaction.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Dynamic interaction of spliceosomal snRNPs with coilin explains Cajal body characteristics — primary. Access: SciSpace primary abstract; Scite primary main body opening plus targeted Results/Discussion excerpts. Claim fit: Coilin/snRNP interaction and RNA-dependent oligomerization, coilin boundary constraint; single-component LLPS model insufficient. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Dynamic control of Cajal body number during zebrafish embryogenesis — primary. Access: Consensus fetched primary abstract + Scite DOI metadata; Scite reader had no text. Claim fit: Zebrafish developmental dynamics, mitotic dispersal/reassembly, separate histone RNA-processing bodies. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
This narrative integrates foundational and recent primary studies available by 12 October 2026. Source access ranges from original abstracts to selected Results, figure captions and Methods, as specified for each reference. It is a scholarly synthesis of the measured systems; it does not independently reproduce their experiments, analyze their raw data or establish exhaustive literature coverage.
Sources and access depth (14)
Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure — primary. Access: Prior audit original Results, Figure 3 and negative-stain Methods; source ledger re-read.. Claim fit: Reconstituted 167/197-bp repeat arrays, H5-dependent compaction and geometry.. Limits: Artificial arrays and negative-stain EM; no direct living-cell fiber census.
Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Chemically defined H4K16-acetylated arrays inhibit folding and cross-fiber interactions and alter ACF remodeling.. Limits: Defined in-vitro substrate; not evidence that all acetylation effects in cells are direct fiber unfolding.
Organization of Chromatin by Intrinsic and Regulated Phase Separation — primary. Access: Prior audit original Results/Discussion and browser Figures 2, 5 and 7; ledger re-read.. Claim fit: Nucleosome-array droplet reconstitution, salt/concentration dependence, H1 and acetylation effects; internal versus whole-droplet recovery.. Limits: Purified arrays under stated conditions; a cellular phase mechanism is not inferred for all chromatin.
Structure of native chromatin fibres revealed by Cryo-ET in situ — primary. Access: Prior audit original selected Results and Methods; ledger re-read.. Claim fit: Cryo-ET in interphase CEM cells reveals heterogeneous local zigzag organization near the envelope.. Limits: Limited cryogenic volumes and cellular model; local arrangements do not define a genome-wide polymer conformation.
Molecular architecture of heterochromatin at the nuclear periphery of primary human cells — primary. Access: Prior audit original publisher Results and Methods; ledger re-read.. Claim fit: Resting primary human CD4+ T-cell peripheral chromatin, heterogeneous elongated arrangement and frequent nucleosome stacking.. Limits: Selected cellular region and quiescent state; observed envelope width is not proof of canonical fiber periodicity.
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization — primary. Access: Prior audit selected original model Results and Methods; ledger re-read.. Claim fit: Brownian bead-spring polymer with reversible multivalent bridging can form clusters without direct protein attraction.. Limits: Coarse-grained equilibrium model; not proof that a specific nuclear assembly is produced by bridging.
Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin — primary. Access: Prior audit original abstract and selected Methods; ledger re-read.. Claim fit: Purified human HP1α, DNA, phosphorylation and partner partitioning demonstrate context-dependent droplet capacity.. Limits: In-vitro capacity is distinguished from a general mammalian cellular mechanism.
Phase separation drives heterochromatin domain formation — primary. Access: Prior audit original abstract; source narrative and ledger re-read.. Claim fit: Drosophila HP1a reconstitution and early embryonic liquid-like heterochromatin observations.. Limits: Early fly developmental context; detailed quantitative Methods not reappraised.
1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells — primary. Access: Prior audit selected original body passages; ledger re-read.. Claim fit: Histone-marker chromatin motion and compaction responses to hexanediol in human cell models.. Limits: Drug sensitivity is not a selective perturbation of phase separation.
HP1 loses its chromatin clustering and phase separation function across evolution — primary. Access: Original publisher abstract and main Results on homolog comparison, phase diagrams and cellular coalescence inspected in this rewrite; earlier audit also read selected Results.. Claim fit: Side-by-side Swi6, fly HP1a and mouse HP1α comparisons, paralog antagonism and heterologous fibroblast tests.. Limits: GFP fusion/reconstitution and heterologous-expression contexts; not a census of all tissues or all HP1 functions.
Biomolecular condensates: organizers of cellular biochemistry — seminal review. Access: Consensus fetched review abstract; publisher body unavailable through web reader.. Claim fit: Definitions of membraneless concentration, multivalency and phase separation as an organizing framework.. Limits: Foundational framework; specific chromatin mechanisms are supported by primary experiments separately.
Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins — primary. Access: Consensus fetched original abstract inspected.. Claim fit: HP1 chromodomain recognition of H3K9 methylation; Suv39h-double-null primary mouse fibroblast localization and catalytic rescue.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Specific methyl-lysine recognition and chromodomain-mutant comparisons; fission-yeast silencing context.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (3)
10.1038/nature16505 — primary research. Access: primary abstract and indexed primary results. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Official publisher abstract and indexed primary PMC4871117 Results checked for eight remodelers, Chd1/Chd2 distribution, promoter-class expression responses and opposing Brg1/Chd4 accessibility effects.
10.1038/s41588-021-00777-3 — primary research. Access: primary abstract and indexed primary results. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite returned no readable body; official publisher abstract and indexed primary PMC7614082 Results support HAP1 accessibility changes, expression/acetylation lag and few early nascent-transcription changes.
SWI/SNF-dependent genes are defined by their chromatin landscape — primary experiment. Access: Consensus fetched primary abstract and Scite identity metadata inspected; Scite returned no readable body. Retained new claims are restricted to the primary abstract.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (6)
10.1038/s41586-019-1275-3 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41586-019-1454-2 — editorial notice. Access: publisher notice metadata plus preceding recorded notice appraisal. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Direct publisher recheck on12October2026 exposed metadata and subscription preview. Exact figure-label scope comes from the preceding7October2026 recorded notice appraisal; no new full-notice body access claimed.
10.1073/pnas.1717730115 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1083/jcb.201801048 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41467-026-75087-5 — primary research. Access: primary publisher results and methods. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Official publisher article published3July2026 volume17article5844. Results, reconstruction limitations and main Methods inspected; 2026 retained despite Consensus record indexing2025.
Cell type–specific 3D-genome organization and transcription regulation in the brain — primary imaging and perturbation. Access: Consensus fetched primary abstract and Scite selected Introduction and initial Results inspected, including combined DNA/RNA-MERFISH in mouse primary motor cortex.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
The TIMELESS and PARP1 interaction suppresses replication-associated DNA gap accumulation — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Saldanha and colleagues acutely depleted TIMELESS or disrupted its interaction with PARP1. The tested cells accumulated post-replicative single-stranded DNA gaps associated with defective Okazaki-fragment processing and impaired XRCC1 recruitment. This places a particular replisome interaction upstream of a backup processing response; it does not equate a DNA gap with a double-strand break or establish a clinical response to PARP inhibition. Saldanha et al. (2024) .
Phase separation of 53BP1 determines liquid‐like behavior of DNA repair compartments — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: 53BP1 dynamics and distinct perturbation response from upstream marks; optoDroplets/signaling not every repaired lesion or unique endogenous phase mechanism.
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Chin Sang and colleagues reconstituted DNA-dependent PARP1 condensates from recombinant human repair proteins and measured enhanced DNA ligation under their in-vitro conditions. This adds a biochemical endpoint to enrichment and material observations. The experiment concerns single-strand repair proteins and defined substrates; it does not validate every 53BP1 focus as a productive double-strand-break repair compartment. Chin Sang et al. (2024) .
Megabase Chromatin Domains Involved in DNA Double-Strand Breaks in Vivo — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Radiation/local damage-associated gamma-H2AX chromatin foci; not DNA backbone continuity or universal one-focus/one-break calibration.
Phase separation of 53BP1 determines liquid‐like behavior of DNA repair compartments — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: 53BP1 dynamics and distinct perturbation response from upstream marks; optoDroplets/signaling not every repaired lesion or unique endogenous phase mechanism.
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
XRCC1 prevents toxic PARP1 trapping during DNA base excision repair — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: XRCC1-associated complexes limit detrimental PARP1 trapping at BER intermediates in deficient models; not universal PARP dispensability.
The TIMELESS and PARP1 interaction suppresses replication-associated DNA gap accumulation — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Saldanha and colleagues linked the TIMELESS–PARP1 interaction to PAR production, XRCC1 recruitment and suppression of post-replicative DNA gaps when Okazaki-fragment processing was challenged. The perturbation defines an interaction-dependent backup route in the tested cells. It should remain separate from 53BP1-dependent end resection, which involves a different intermediate and endpoint. Saldanha et al. (2024) .
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures — primary study. Access: Bibliographic metadata and primary abstract via SciSpace/discovery where available; full-text retrieval failed after Scite quota.. Claim fit: The 3D-SPARK study combined nucleotide-analogue pulse labeling and super-resolution imaging to classify DNA-synthesis nanostructures in individual human cells. Reported size, abundance and spatial arrangement changed under several perturbations. These are labeled synthesis structures measured over specified pulses; the result does not turn every optical object into a mapped replication origin or replace a DNA-fibre measure of fork progression. Hawgood et al. (2025) .
Dynamics of DNA Replication Factories in Living Cells — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: GFP-PCNA live-cell replication-site assembly/disassembly and positional stability; physical anchors and universal focus units not identified.
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Scientific text and references appraised at recorded source depth · research
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (4)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary experimental research. Access: Scite primary abstract; root independently read actual PMC5127388 main Results, Fig2E and main Methods on 12 October; supplements not read. Claim fit: Xenopus nucleoli plus NPM1/FIB1/RNA reconstitution, two reconstituted condensed phases and solution, component differences; R=50-nm probe particles in vitro, in-vivo fusion constrains viscosity/surface-tension ratio
RNA buffers the phase separation behavior of prion-like RNA binding proteins — primary experimental research. Access: Scite primary abstract and actual indexed figure captions. Claim fit: Low/high RNA ratios have different effects on RBP demixing, with nuclear RNA-buffering interpretation; no universal clinical cause
Paraspeckle condensation is controlled via TDP-43 polymerization and linked to neuroprotection — primary experimental research. Access: Consensus fetched primary abstract; Scite primary main Results beginning. Claim fit: Concentration/polymerization/RNA-binding-dependent paraspeckle regulation; repeat deletion and stressed human-neuron cytoprotection, patient survival association not clinical efficacy
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Scientific text and references appraised at recorded source depth · research
RNA processing provides a newer way to test nuclear-body architecture
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (7)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary study. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.
Compositional Control of Phase-Separated Cellular Bodies — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Engineered multivalent scaffold/client partitioning, valency and stoichiometry, with analogous PML/P-body observations; not every endogenous body.
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Quinodoz and colleagues mapped successive rRNA processing stages and generated engineered nucleoli. Small-subunit processing defects reordered nucleolar layers and prevented normal rRNA outflux. This connects RNA maturation to architecture more directly than a droplet-shape comparison, while remaining a specific nucleolar result rather than evidence for one assembly mechanism across all nuclear bodies. Quinodoz et al. (2025) .
The fork protection complex promotes parental histone recycling and epigenetic memory — primary experiment. Access: Consensus fetched primary abstract; Scite Introduction, main-text study summary, Figure 1 caption and initial Results inspected. Supplementary validation and raw data not reanalyzed.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
This narrative integrates foundational and recent primary studies available by 12 October 2026. Source access ranges from original abstracts to selected Results, figure captions and Methods, as specified for each reference. It is a scholarly synthesis of the measured systems; it does not independently reproduce their experiments, analyze their raw data or establish exhaustive literature coverage.
Sources and access depth (11)
Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Chemically defined H4K16-acetylated arrays inhibit folding and cross-fiber interactions and alter ACF remodeling.. Limits: Defined in-vitro substrate; not evidence that all acetylation effects in cells are direct fiber unfolding.
Nuclear receptor co-repressors are required for the histone-deacetylase activity of HDAC3 in vivo — primary. Access: Prior audit original selected main Results, captions and Discussion; ledger re-read.. Claim fit: NCoR/SMRT activation-domain mutant mice separate retained HDAC3 protein from detectable deacetylase activity; tissue/occupancy context.. Limits: Recruitment also changes; activity below assay background cannot be excluded and all HDACs are not equivalent.
An assessment of histone-modification antibody quality — primary. Access: Consensus fetched original abstract and publisher abstract/issue date inspected.. Claim fit: Empirical antibody specificity and ChIP-performance tests across fly, worm and human systems.. Limits: The reported failure fractions describe the tested panel, not all present-day antibodies.
Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains — primary. Access: Prior audit original selected main Results, captions and Discussion; ledger re-read.. Claim fit: H3K9ac profiles in postmortem DLPFC gray matter from 669 ROS/MAP participants, tau/amyloid comparisons and model-system observations.. Limits: Cross-sectional bulk tissue; architecture references from other specimens; model directionality differs from human tissue and raw data were not reanalyzed.
Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease — primary. Access: Prior audit original publisher abstract; ledger re-read.. Claim fit: H4K16ac comparisons among human temporal-lobe young, elderly cognitively normal and Alzheimer groups.. Limits: Abstract-bounded cross-sectional observations; full main Results/covariates and within-person trajectories not appraised.
CHAS infers cell type-specific signatures in bulk brain histone acetylation studies of neurological and psychiatric disorders — primary. Access: Prior audit original abstract and selected indexed Results/method description; current Consensus fetched identity record inspected.. Claim fit: Reference-based inference of cellular components in bulk brain histone-acetylation profiles.. Limits: Deconvolution depends on reference representativeness and model assumptions; not direct purified-cell measurement.
ACSS2 upregulation enhances neuronal resilience to aging and tau-associated neurodegeneration — primary. Access: Consensus fetched original abstract plus publisher Results/Figures 1–3 and initial mouse-intervention Results inspected; publisher date 9 January 2026 verified.. Claim fit: Cultured hippocampal-neuron and P301S mouse ACSS2 increase, histone-acetylation/transcription changes, tau-associated resilience and memory/LTP outcomes.. Limits: Preclinical neuronal and mouse systems, including early intervention; not a human therapeutic efficacy finding.
Histone deacetylase inhibitors arrest polyglutamine-dependent neurodegeneration in Drosophila — primary. Access: Consensus search and fetched original abstract inspected.. Claim fit: Huntingtin-exon-1 acetyltransferase interactions, cell acetylation changes and rescue of fly polyglutamine phenotypes.. Limits: Cell-free, cultured-cell and fly-model evidence; no human therapeutic efficacy claimed.
Targeting H3K4 trimethylation in Huntington disease — primary. Access: SciSpace indexed original abstract and exact DOI/title/author identity inspected.. Claim fit: H3K4me3 changes in HD mouse/human brain and SMCX/Jarid1c perturbation in primary neurons/fly models.. Limits: Association in human tissue and causal perturbation in models are distinguished; complete Results and supplements not appraised.
Mitochondrial dysfunction–induced H3K27 hyperacetylation perturbs enhancers in Parkinson’s disease — primary. Access: SciSpace original abstract and publisher selected main Results on mitochondrial perturbations and H3K27/H3K36 comparisons inspected.. Claim fit: Chemically/genetically perturbed dopaminergic models, MitoPark comparisons and postmortem H3K27ac association.. Limits: Patient association is not a longitudinal causal experiment; N27/mitochondrial models capture selected disease mechanisms.
This narrative integrates foundational and recent primary studies available by 12 October 2026. Source access ranges from original abstracts to selected Results, figure captions and Methods, as specified for each reference. It is a scholarly synthesis of the measured systems; it does not independently reproduce their experiments, analyze their raw data or establish exhaustive literature coverage.
Sources and access depth (21)
Crystal structure of the nucleosome core particle at 2.8 Å resolution — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Histone octamer, DNA superhelix and histone-tail contacts in the crystallized nucleosome.. Limits: Crystallized core particle; not a direct measurement of chromatin dynamics or whole-nucleus packing.
Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure — primary. Access: Prior audit original Results, Figure 3 and negative-stain Methods; source ledger re-read.. Claim fit: Reconstituted 167/197-bp repeat arrays, H5-dependent compaction and geometry.. Limits: Artificial arrays and negative-stain EM; no direct living-cell fiber census.
Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Chemically defined H4K16-acetylated arrays inhibit folding and cross-fiber interactions and alter ACF remodeling.. Limits: Defined in-vitro substrate; not evidence that all acetylation effects in cells are direct fiber unfolding.
Organization of Chromatin by Intrinsic and Regulated Phase Separation — primary. Access: Prior audit original Results/Discussion and browser Figures 2, 5 and 7; ledger re-read.. Claim fit: Nucleosome-array droplet reconstitution, salt/concentration dependence, H1 and acetylation effects; internal versus whole-droplet recovery.. Limits: Purified arrays under stated conditions; a cellular phase mechanism is not inferred for all chromatin.
Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins — primary. Access: Consensus fetched original abstract inspected.. Claim fit: HP1 chromodomain recognition of H3K9 methylation; Suv39h-double-null primary mouse fibroblast localization and catalytic rescue.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Specific methyl-lysine recognition and chromodomain-mutant comparisons; fission-yeast silencing context.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Role of the polycomb protein Eed in the propagation of repressive histone marks — primary. Access: Consensus fetched original abstract inspected.. Claim fit: EED recognition of repressive trimethyl-lysine marks and allosteric PRC2 activation; biochemical and fly-mutant evidence.. Limits: Reader–writer propagation model; does not alone prove a complete cellular inheritance mechanism.
Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells — primary. Access: Consensus search and fetched original abstract inspected; publisher body access failed.. Claim fit: Acute H3K9 methyltransferase depletion in engineered mESCs, heterogeneous mark decay and HP1 threshold-associated opening.. Limits: Abstract-bounded; four stability classes in this engineered pluripotent-cell context, not universal decay constants.
Histone modifications at human enhancers reflect global cell-type-specific gene expression — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Multi-cell-type chromatin maps and enhancer activity associate enhancer signatures with cell-specific expression programs.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
SWI/SNF-dependent genes are defined by their chromatin landscape — primary. Access: Prior audit fetched original Consensus abstract; identity checked against indexed DOI metadata.. Claim fit: Chromatin landscape association with gene-specific SWI/SNF dependence; claims restricted to original abstract.. Limits: No complete original main Results or supplementary analysis inspected.
Two distinct modes for propagation of histone PTMs across the cell cycle — primary. Access: Prior audit original main Results, Figures 1–4 and Discussion; ledger re-read.. Claim fit: Nascent-chromatin isotope/mass-spectrometry study distinguishes parental and new histone modification kinetics.. Limits: Population peptides, not genomic address or every pair of modifications on one nucleosome; supplementary cell-line details not appraised.
Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction — primary. Access: Prior audit original selected Results and Discussion; ledger re-read.. Claim fit: mESC H1c/d/e-depleted comparison, chromatin compaction and delayed H3K27me3 restoration on replicated DNA.. Limits: Ensemble occupancy and fitted restoration rates; chronic depletion may have indirect effects.
The fork protection complex promotes parental histone recycling and epigenetic memory — primary. Access: Prior audit fetched original abstract and selected main Results/Figure 1; ledger re-read.. Claim fit: Fork-protection-complex contribution to parental histone recycling and epigenetic-memory maintenance.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Chromatin Modifications and Their Function — seminal review. Access: Fetched Consensus review abstract and author-review PDF hosted by UC Berkeley inspected, including introductory chemical classes and causal/epigenetic caveats.. Claim fit: Foundational classification of chemical modifications, reader recruitment, contact changes and context-dependent interpretation.. Limits: Historical review used for foundational principles; current claims cite original studies.
Nuclear receptor co-repressors are required for the histone-deacetylase activity of HDAC3 in vivo — primary. Access: Prior audit original selected main Results, captions and Discussion; ledger re-read.. Claim fit: NCoR/SMRT activation-domain mutant mice separate retained HDAC3 protein from detectable deacetylase activity; tissue/occupancy context.. Limits: Recruitment also changes; activity below assay background cannot be excluded and all HDACs are not equivalent.
An assessment of histone-modification antibody quality — primary. Access: Consensus fetched original abstract and publisher abstract/issue date inspected.. Claim fit: Empirical antibody specificity and ChIP-performance tests across fly, worm and human systems.. Limits: The reported failure fractions describe the tested panel, not all present-day antibodies.
Metabolic regulation of gene expression by histone lactylation — primary. Access: Consensus fetched original abstract inspected.. Claim fit: Histone lysine lactylation identification in human/mouse cells and temporal transcriptional response in challenged M1 macrophages.. Limits: Abstract-bounded; the proposed lactate-clock mechanism is model/system-specific rather than a universal response.
The alanyl-tRNA synthetase AARS1 moonlights as a lactyltransferase to promote YAP signaling in gastric cancer — primary. Access: Consensus fetched original abstract inspected; publisher body request timed out.. Claim fit: Direct lactate/ATP-dependent protein lactylation and YAP–TEAD substrates in gastric-cancer context.. Limits: Nonhistone substrate findings must not be redescribed as direct evidence of histone lactylation in every tissue.
Megabase Chromatin Domains Involved in DNA Double-Strand Breaks in Vivo — primary. Access: Consensus fetched original abstract inspected.. Claim fit: H2AX Ser139 phosphorylation and damage-associated domains in irradiation/microbeam comparisons.. Limits: Damage-response chromatin domain is not a direct count of repair completion or a one-to-one statement for every lesion class.
Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures — primary. Access: Original abstract in Consensus search read; fetched bibliographic record confirms identity and includes takeaway only.. Claim fit: Twenty-feature maps at defined human DSB sites; repair-associated signatures and H2BK120 ubiquitination-to-acetylation switch.. Limits: Original abstract supports attributed associations; complete Results and supplements not appraised.
The molecular architecture of lamins in somatic cells — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Prepared vimentin-null mouse-fibroblast lamina filament structure; approximately3.5nm filaments are not live-lamina thickness.
Lamin B1 loss is a senescence-associated biomarker — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: LaminB1 decrease in defined fibroblast senescence states and irradiated-mouse tissue; no standalone individual-cell diagnosis or ordinary ageing equivalence.
Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction — primary study. Access: Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.. Claim fit: LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.
Imaging-Based Molecular Interaction Between Src and Lamin A/C Mechanosensitive Proteins in the Nucleus of Laminopathic Cells — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Petrini and colleagues examined skin fibroblasts from two laminopathic patients. Confocal/STED co-distribution and antibody-based lifetime/FRET measurements supported closer association of Src and lamin A/C in the tested patient samples. The small, defined comparison does not establish a universal mutation effect, a mechanical modulus or a causal mechanism of ordinary ageing. Petrini et al. (2024) .
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction — primary study. Access: Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.. Claim fit: LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.
Imaging-Based Molecular Interaction Between Src and Lamin A/C Mechanosensitive Proteins in the Nucleus of Laminopathic Cells — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: A 2024 study compared skin cells from two people with laminopathies and comparison cells. Fluorescence measurements indicated closer association between lamin A/C and another protein, Src, in those samples. This shows another measurable cellular difference; the images do not by themselves prove why a patient develops disease or provide a test for every laminopathy. Petrini et al. (2024) .
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction — primary study. Access: Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.. Claim fit: LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.
Imaging-Based Molecular Interaction Between Src and Lamin A/C Mechanosensitive Proteins in the Nucleus of Laminopathic Cells — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Petrini and colleagues studied fibroblasts from two laminopathic patients with confocal/STED microscopy and lifetime-based FRET. Their results supported a stronger Src–lamin A/C association in the tested patient cells. Co-distribution measures spatial overlap, while FRET constrains proximity of the labels; neither readout alone measures nuclear stiffness or establishes the mechanism of every LMNA-associated disease. Petrini et al. (2024) .
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
The molecular architecture of lamins in somatic cells — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Prepared vimentin-null mouse-fibroblast lamina filament structure; approximately3.5nm filaments are not live-lamina thickness.
Structure and gating of the nuclear pore complex — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Xenopus oocyte NPC cryo-tomographic scaffold/channel structure; not direct universal transport kinetics.
Simple rules for passive diffusion through the nuclear pore complex — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.
Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction — primary study. Access: Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.. Claim fit: LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.
Imaging-Based Molecular Interaction Between Src and Lamin A/C Mechanosensitive Proteins in the Nucleus of Laminopathic Cells — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Petrini and colleagues reported increased Src–lamin A/C co-distribution and altered donor-fluorescence lifetime in skin fibroblasts from two laminopathic patients. The association adds a bounded molecular readout to the older genetics and null-cell comparisons. Antibody-labeled proximity and co-distribution do not independently establish a shared force-transmission defect, a diagnostic threshold or patient treatment benefit. Petrini et al. (2024) .
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (4)
10.1038/s41467-023-39846-y — primary research. Access: selected primary body and indexed results. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected primarybody inspected; indexedPMC10333366Results independently confirm H1e/H3K27me3regional associations, partialH1c/d/e-loss with unchangedSUZ12, restoration/mark/mRNA distinctions. Full supplementalmechanistic validation not reproduced.
10.1038/s41467-023-42072-1 — primary research. Access: selected primary body and indexed results methods. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite first body page and official indexed primary Results/Discussion/Methods support frozen CEM periphery, variable20–50nm arrangements, relaxed zigzags and partial linker/H1 resolution. PrimaryTable1 and classificationMethods confirm5tomograms and6790selectedparticles. Sampling limits retained.
10.1038/s41467-026-75087-5 — primary research. Access: primary publisher results and methods. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Official publisher article published3July2026 volume17article5844. Results, reconstruction limitations and main Methods inspected; 2026 retained despite Consensus record indexing2025.
MINFLUX dissects nucleosome and compacting chromatin structures in living cells — primary method and experiment. Access: Scite primary body: Introduction, Results and Discussion inspected; supplementary data and raw localizations not reanalyzed.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (4)
10.1016/j.celrep.2016.04.085 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1016/j.cell.2017.09.026 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41586-023-05961-5 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
Uniform dynamics of cohesin-mediated loop extrusion in living human cells — primary experiment and model. Access: Consensus fetched primary abstract and Scite selected main-text passages, including study design and initial Results; not every supplementary analysis inspected.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (4)
10.1016/j.celrep.2016.04.085 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1016/j.cell.2017.09.026 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41586-023-05961-5 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
Uniform dynamics of cohesin-mediated loop extrusion in living human cells — primary experiment and model. Access: Consensus fetched primary abstract and Scite selected main-text passages, including study design and initial Results; not every supplementary analysis inspected.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies.
Mapping eGFP Oligomer Mobility in Living Cell Nuclei — primary. Access: Primary PLOS main Abstract, Methods data analysis/acquisition/calibration and selected Results/Discussion; no raw data reanalysis.. Claim fit: eGFP oligomer FCS outside nucleoli: calibrated two-normal-diffusion components plus triplet term; cell/model/probe constraints retained.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
A Molecular Sensor Reveals Differences in Macromolecular Crowding between the Cytoplasm and Nucleoplasm — primary. Access: Publisher primary abstract, author metadata and list of supplemental controls; complete Results not accessible. Journal article distinguished from same-title conference abstract.. Claim fit: Oligonucleotide FRET sensor, in-vitro crowder responses and compartment/perturbation contrasts; signal reflects calibrated sensor behavior rather than universal mass density.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes — primary. Access: Fetched primary abstract and publisher Results excerpts on Xenopus assembly and density model; Crossmark publication date and author metadata checked. Complete body and supplements not appraised.. Claim fit: Nuclear/cytoplasmic density differences and pressure-balance model constrained by transport, chromatin and embryo observations. Erroneous2023 provider year corrected to publisher15August2025.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Osmotic pressure regulates DNA labelling and transcription with dCas9-SunTag system in live cells — primary. Access: Fetched primary abstract and publisher search excerpts of Results on labeling/binding and Discussion; full Methods not appraised. Online26November2025; volume17/article773 version of record21January2026.. Claim fit: Osmotic perturbation of engineered dCas9-SunTag DNA labeling/transcription, binding-unbinding interpretation and chromatin-motion/intensity proxies; not universal transcription law or direct excluded-volume measurement.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Chromatin compaction during confined cell migration induces and reshapes nuclear condensates — primary. Access: Primary publisher Abstract and main Results/Figures1–4 read; complete Methods and supplements not appraised.. Claim fit: MDA-MB-231 microfluidic confinement, differential leading/trailing chromatin heterogeneity and endogenous/synthetic condensate behavior; reporter expression and phase-boundary context matter.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility — primary. Access: Published identity and primary abstract from author-manuscript repository; full main text not appraised.. Claim fit: Differently sized inert GFP probes and polymer simulations; size-dependent intermediate-scale viscoelastic behavior and obstacle-network model; not universal fixed fractal organization.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy — primary. Access: Bibliographic metadata and primary abstract via SciSpace/discovery where available; full-text retrieval failed after Scite quota.. Claim fit: Rahman and colleagues found that apparent co-enrichment of some nuclear targets depended on the scale used for multiplexed imaging analysis. A pair correlated over larger distances could become uncorrelated or partitioned at shorter distances. This supports retaining measurement scale when discussing crowded domains; a fluorescence spatial correlation is not an independent measurement of excluded volume, binding affinity or material viscosity. Rahman et al. (2025) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
A sensor for quantification of macromolecular crowding in living cells — primary. Access: Fetched primary abstract and identity; full methods not read.. Claim fit: Genetically encoded FRET crowding sensor in bacterial and mammalian cells; assay principle does not supply nuclear-specific values.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Robust model-based analysis of single-particle tracking experiments with Spot-On — primary. Access: Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.. Claim fit: Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force — primary. Access: Primary manuscript main Summary, Results on microrheology and mechanomemory, Figures 1–5 and Discussion read; supplemental figures and raw measurements not reanalysed.. Claim fit: 200-nm-diameter targeted magnetic particles in CHO DHFR reporter nuclei; 0.1–5 Hz force response and separate hiPSC Pol II arm; local perturbation and injection limitations.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1 — primary. Access: Published PDF front matter, main preparation/treatment Methods, Results around Figure 9 and Discussion read; supplementary data not appraised.. Claim fit: Metabolically active karyoplast compression/dissipation and BRM-014 inhibition; BRM-014 inhibits BRM and BRG1, so pharmacology is not exclusive genetic proof for BRG1. Karyoplasts are not bare detergent-isolated nuclei.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
This narrative integrates foundational and recent primary studies available by 12 October 2026. Source access ranges from original abstracts to selected Results, figure captions and Methods, as specified for each reference. It is a scholarly synthesis of the measured systems; it does not independently reproduce their experiments, analyze their raw data or establish exhaustive literature coverage.
Sources and access depth (11)
A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro — primary. Access: Original PubMed abstract inspected in this rewrite.. Claim fit: Xenopus egg-extract XCAP-C/E association, chromosomal axis localization, antibody-blocking effects on assembly and maintenance.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Reconstitution of mitotic chromatids with a minimum set of purified factors — primary. Access: Original PubMed abstract and SciSpace indexed primary abstract inspected.. Claim fit: Six-factor reconstitution, embryonic H2A.X-F/FACT substrate dependence and condensin-I Cdk1 phosphorylation; sufficiency in the defined preparation.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Real-time imaging of DNA loop extrusion by condensin — primary. Access: Consensus search and fetched original abstract inspected in this rewrite.. Claim fit: Direct purified yeast-condensin loop extrusion on DNA; ATP dependence, asymmetry and force-dependent behavior.. Limits: Purified DNA assay; cellular loop paths and complete chromosome assembly not directly observed.
A pathway for mitotic chromosome formation — primary. Access: Prior audit selected original Results and Figures 1–5; reference ledger and source-linked narrative re-read for this rewrite.. Claim fit: Synchronized DT40 mitotic Hi-C, condensin depletion and hierarchical loop-model interpretation.. Limits: Population contacts and polymer-model fit; supplements and raw contact data not reanalyzed.
A quantitative map of human Condensins provides new insights into mitotic chromosome architecture — primary. Access: Prior audit original main Results, captions and Discussion; ledger and narrative re-read.. Claim fit: HeLa Kyoto endogenous condensin numbers, axial localization and mitotic association dynamics; loop paths remain hypothetical.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Rules of engagement for condensins and cohesins guide mitotic chromosome formation — primary. Access: Prior audit fetched Consensus original abstract and selected original main Results; source ledger re-read.. Claim fit: DT40 condensin/cohesin engagement, compaction versus rod individualization, and integrated model interpretation.. Limits: Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed.
Functional interplay between condensin I and topoisomerase IIα in single-molecule DNA compaction — primary. Access: Consensus search and fetched original abstract inspected; publisher body access failed and was not claimed. Independent reviewer inspected primary Figure 7 and Discussion for the topological inference.. Claim fit: Purified condensin-I/topoisomerase-IIα compact structures, C-terminal-domain dependence, protease resistance and enzymatic resolution consistent with knot formation; knots were not directly visualized.. Limits: Naked-DNA single-molecule system; cellular topological resolution cannot be inferred from knots in a reconstitution.
Distinct functions of condensin I and II in mitotic chromosome assembly — primary. Access: SciSpace indexed original abstract inspected; exact DOI/title identity checked.. Claim fit: Mammalian prophase condensin-II access, condensin-I recruitment after nuclear-envelope breakdown and RNAi timing phenotypes.. Limits: Source abstract; detailed cell-line and depletion-efficiency claims omitted.
Establishment of dsDNA-dsDNA interactions by the condensin complex — primary. Access: SciSpace indexed original abstract and fetched Consensus bibliographic record inspected; original DOI and title matched.. Claim fit: Purified fission-yeast sequential dsDNA capture and complementary cellular contacts motivate a diffusion-capture alternative.. Limits: Abstract-bounded interpretation; not evidence that all cellular chromosome construction uses capture instead of extrusion.
Condensin restructures chromosomes in preparation for meiotic divisions — primary. Access: SciSpace original abstract and exact DOI/title/author metadata inspected.. Claim fit: C. elegans meiotic chromosome remodeling after recombination, resolution of defined linkages and individualized bivalents.. Limits: Original abstract-bounded; not a claim that all meiotic species share vertebrate mitotic architecture.
Scientific text and references appraised at recorded source depth · research
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (4)
Mediator and RNA polymerase II clusters associate in transcription-dependent condensates — primary experimental research. Access: Scite indexed primary figure captions and targeted excerpts; recorded body text only 4,760 characters, not full original main article. Claim fit: mESC endogenous clusters, JQ1/DRB dependencies, six-cell Esrrb proximity, recovery/merging; exchange and proximity not uniquely a phase mechanism
Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin — primary experimental research. Access: SciSpace primary abstract; Scite main body and selected primary Results excerpts. Claim fit: NDF–FACT biochemical/single-molecule elongation and human stem-cell perturbations; named elongation system, not all Pol II clustering
A single cluster of RNA Polymerase II molecules is stably associated with active genes — primary experimental research. Access: Consensus fetched record + Scite primary abstract; official publisher main Results/Discussion read. Claim fit: Fly-embryo Pol II clustering explained by engaged-polymerase accumulation with imaging and simulations; ordinary clusters distinct from histone locus bodies; publisher date resolves Consensus 2025 metadata discrepancy
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Mitochondria-derived nuclear ATP surge protects against confinement-induced proliferation defects — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: The Ghose et al. (2025) reported actin-dependent mitochondrial repositioning around the nucleus and a nuclear ATP increase in its cell models. The actin-dependent organelle arrangement is a separate observation from the damage-induced intranuclear filaments of Belin and colleagues. It does not locate those filaments at every repair site or show that all nuclear ATP production uses an intranuclear actin network. Ghose et al. (2025) .
This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies.
Sources and access depth (29)
Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Nuclear envelope rupture and repair during cancer cell migration — primary. Access: Primary author-manuscript main Abstract/Results pages1–4 and Figures1/2/4; supplementary Methods and raw data not reanalysed.. Claim fit: NLS-reporter rupture, defined in-vitro and mouse-dermis models, deformation-associated damage foci and ESCRT-III-dependent resealing independently match primary main Results/Figures. Mixed-topic Scite opening excluded.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force — primary. Access: Primary manuscript main Summary, Results on microrheology and mechanomemory, Figures 1–5 and Discussion read; supplemental figures and raw measurements not reanalysed.. Claim fit: 200-nm-diameter targeted magnetic particles in CHO DHFR reporter nuclei; 0.1–5 Hz force response and separate hiPSC Pol II arm; local perturbation and injection limitations.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1 — primary. Access: Published PDF front matter, main preparation/treatment Methods, Results around Figure 9 and Discussion read; supplementary data not appraised.. Claim fit: Metabolically active karyoplast compression/dissipation and BRM-014 inhibition; BRM-014 inhibits BRM and BRG1, so pharmacology is not exclusive genetic proof for BRG1. Karyoplasts are not bare detergent-isolated nuclei.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes — primary. Access: Fetched primary abstract and publisher Results excerpts on Xenopus assembly and density model; Crossmark publication date and author metadata checked. Complete body and supplements not appraised.. Claim fit: Nuclear/cytoplasmic density differences and pressure-balance model constrained by transport, chromatin and embryo observations. Erroneous2023 provider year corrected to publisher15August2025.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Heterogeneous force response of chromatin in isolated nuclei. — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Bergamaschi and colleagues measured isolated-nucleus force responses together with chromatin and nuclear-envelope deformation. Chromatin was more compliant than the envelope below the reported 30% strain regime, and chromatin digestion softened nuclei. The joint readouts strengthen component interpretation in the tested preparation without defining one elastic modulus or viscosity for every nucleus. Bergamaschi et al. (2024) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Attar and colleagues used polymer simulations compared with micromechanical and chromosome-contact measurements. In that model, peripheral chromatin attachment transmitted imposed nuclear forces to chromatin, and internal crosslinks stiffened the nucleus only when that peripheral coupling was present. This is a model-constrained account of load transfer; a mapped lamina association by itself does not establish the strength or permanence of every molecular tether. Attar et al. (2025) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis — primary. Access: Publisher primary Abstract and main Results through heterochromatin-tether deconvolution, membrane LAP2 rescue and short/long-term transcription effects read; complete Methods and supplements not appraised. Published 24 February 2026.. Claim fit: Redundant LBR/membrane LAP2 tethering in mammalian cell models, distinction between short-term release and persistent loss; not universal instant repression by peripheral position.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Chromatin compaction during confined cell migration induces and reshapes nuclear condensates — primary. Access: Primary publisher Abstract and main Results/Figures1–4 read; complete Methods and supplements not appraised.. Claim fit: MDA-MB-231 microfluidic confinement, differential leading/trailing chromatin heterogeneity and endogenous/synthetic condensate behavior; reporter expression and phase-boundary context matter.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Visualizing nuclear pore complex plasticity with pan-expansion microscopy — primary. Access: Fetched primary abstract and publication record; full Methods and Results not yet appraised.. Claim fit: Expanded fixed-cell NPC diameter distributions, nuclear-surface bias, hyperosmotic constriction and LINC perturbation; one patient-derived neuronal comparison does not establish all ALS.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Mapping eGFP Oligomer Mobility in Living Cell Nuclei — primary. Access: Primary PLOS main Abstract, Methods data analysis/acquisition/calibration and selected Results/Discussion; no raw data reanalysis.. Claim fit: eGFP oligomer FCS outside nucleoli: calibrated two-normal-diffusion components plus triplet term; cell/model/probe constraints retained.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility — primary. Access: Published identity and primary abstract from author-manuscript repository; full main text not appraised.. Claim fit: Differently sized inert GFP probes and polymer simulations; size-dependent intermediate-scale viscoelastic behavior and obstacle-network model; not universal fixed fractal organization.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
The molecular architecture of lamins in somatic cells — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Prepared vimentin-null mouse-fibroblast lamina filament structure; approximately3.5nm filaments are not live-lamina thickness.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Architecture of the linker-scaffold in the nuclear pore — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Linker/scaffold structural integration and flexible ring-spoke models; model architecture not universal transport threshold.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Architecture of the cytoplasmic face of the nuclear pore — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Composite human/fungal cytoplasmic-face architecture and approximate composition; not one atomic image of a functioning pore.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: LAD association map, domain scales and low expression in human fibroblasts; no universal permanent tether or repression causality.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions — editorial notice. Access: Primary correction abstract/citation record containing full correction statements; original full Methods not reappraised.. Claim fit: Official corrected H3K9me3 identity and Methods data sources; no inferred change to uncorrected abstract-level LAD conclusions.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Reaction-diffusion FRAP solutions constrain binding inference; not every recovery curve identifies every parameter.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Robust model-based analysis of single-particle tracking experiments with Spot-On — primary. Access: Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.. Claim fit: Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Fluid Mechanics of Microrheology — seminal review. Access: Publisher bibliographic identity and abstract; established mathematical relationships independently checked dimensionally. Detailed review body not appraised.. Claim fit: Foundational synthesis of probe/bulk coupling, passive thermal-fluctuation and active-force microrheology assumptions; not a nuclear measurement.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology — primary. Access: Root independently read primary PMC12173521 Abstract and selected main Methods/Results paragraphs, including oscillatory preparation, hydrodynamic drag correction, morphology and Jeffreys analysis; primary Scite webpage identity corroborated. Supplement and raw-data reanalysis excluded.. Claim fit: Oscillatory AFM on live and isolated MCF7 nuclei, hydrodynamic-drag validation, modulus/loss-tangent distinction and Jeffreys model. The published author list supersedes incomplete Consensus authors.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Coupling of the nucleus and cytoplasm: role of the LINC complex — primary. Access: Primary abstract and bibliographic identity through author institutional repository; full Methods not appraised.. Claim fit: SUN1/SUN2–nesprin2 localization and depletion/overexpression in HeLa cells, perinuclear spacing and LINC model.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores — primary. Access: Publisher primary selected Results on force application and import/export plus AFM Methods excerpt read; complete body and supplements not appraised.. Claim fit: Force-dependent YAP entry in defined fibroblast/MCF10A systems, nuclear deformation and import-rate assays; not all cargo or universal pore-mechanics explanation.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
ESCRT-III controls nuclear envelope reformation — primary. Access: Fetched primary abstract and identity; full Methods not accessible.. Claim fit: CHMP2A/CHMP4B/UFD1-dependent postmitotic envelope sealing and compartmentalization in human cells, not all envelope-repair routes.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Nuclear pore permeability and fluid flow are modulated by its dilation state — primary. Access: Consensus fetched primary record and search-returned primary abstract; full Results inaccessible. Online 2024; issue year should not replace online publication date.. Claim fit: Dictyostelium osmotic adaptation, dilation-dependent pressure-driven nucleocytosolic fluid flow and viral blockage; not identical to diffusion or receptor-driven transport.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Simple rules for passive diffusion through the nuclear pore complex — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells — primary. Access: Primary abstract, publication identity and main Figures1–5 captions through PubMed read; complete main Results/Methods not appraised.. Claim fit: Human embryo/primed-pluripotency models connect growth-factor state, nuclear deformation, crowding and chromatin regulation. Mechanical/osmotic priming is not sufficient for robust lineage induction without sustained biochemical signals.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
This scholarly synthesis integrates foundational studies and literature available by 12 October 2026. Source access ranges from primary abstracts to selected Results, figure captions and Methods, as specified for each reference. Experiments and models retain their organism, construct and perturbation context; raw data and supplementary material have not been comprehensively reanalysed.
Sources and access depth (36)
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary. Access: Consensus fetched primary abstract + Scite metadata; no full body retrieved. Claim fit: Spatial rRNA maturation and synthetic nucleolar organization; RNA as scaffold/substrate, not architecture-only function. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
SON and SRRM2 are essential for nuclear speckle formation — primary. Access: Scite main body and targeted primary Results/figure excerpts. Claim fit: SON/SRRM2 combination disperses speckle proteins in HAP1/HEK293 models; monoclonal SC35 principal speckle target is SRRM2, historic SRSF2 attribution inappropriate. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins — primary. Access: Scite identity; SciSpace primary abstract; root actual PMC3998805 main Results and Fig2/Fig3 captions. Claim fit: Oxidative PML mesh, subsequent SUMO/SIM partner retention, partner SUMOylation and selected RNF4 degradation; narrow CHO shell/core immuno-EM in Fig3B retained. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Dynamic interaction of spliceosomal snRNPs with coilin explains Cajal body characteristics — primary. Access: SciSpace primary abstract; Scite primary main body opening plus targeted Results/Discussion excerpts. Claim fit: Coilin/snRNP interaction and RNA-dependent oligomerization, coilin boundary constraint; single-component LLPS model insufficient. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Coilin-dependent snRNP assembly is essential for zebrafish embryogenesis — primary. Access: Publisher primary abstract, Fig1–7 descriptions and 4 April 2010 inline correction notice. Claim fit: Coilin depletion, developmental and spliced-RNA deficits, rescue by assembled human snRNPs.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Genome organization around nuclear speckles drives mRNA splicing efficiency — primary. Access: Consensus fetched primary abstract; publisher abstract and figure-caption descriptions. Claim fit: Speckle-proximal spliceosome binding and splicing; directed RNA recruitment tests spatial sufficiency.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies — primary. Access: Scite primary main body and targeted Results/figure/Discussion excerpts. Claim fit: HeLa/NIH3T3 prepared-section RNA/protein EM localization; terminal/core organization, cross-wise versus looped alternative unresolved; not cryo-ET or kinetic evidence. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Paraspeckles are constructed as block copolymer micelles — primary. Access: Scite primary abstract. Claim fit: RNA-domain deletion/transcription comparisons plus explicitly proposed micellization model. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Malat1 is not an essential component of nuclear speckles in mice — primary. Access: Primary publication abstract and bibliographic record. Claim fit: Viable fertile knockout mice with retained marker localization under laboratory conditions; contextual necessity.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Nuclear speckles enable processing of RNA from GC-rich isochores — primary. Access: Consensus fetched identity; SciSpace and PubMed primary abstract; actual PMC13283296 selected main Results/Fig1–4 captions. Claim fit: Acute SON/SRRM2 loss in human cells affects short GC-rich intron processing and accumulated RNA more than nascent RNA; protein loss and architecture remain coupled. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Compositional Control of Phase-Separated Cellular Bodies — primary. Access: Scite primary abstract; actual PMC4967043 main Results, scaffold/client comparisons, Fig1–5 descriptions. Claim fit: Specific client binding, scaffold stoichiometry/valency, selective partitioning and different component recovery; model systems do not diagnose all bodies. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary. Access: Scite primary abstract; root independently read actual PMC5127388 main Results, Fig2E and main Methods on 12 October; supplements not read. Claim fit: Xenopus nucleoli plus NPM1/FIB1/RNA reconstitution, two reconstituted condensed phases and solution, component differences; R=50-nm probe particles in vitro, in-vivo fusion constrains viscosity/surface-tension ratio. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Cryo-EM structure of PML RBCC dimer reveals CC-mediated octopus-like nuclear body assembly mechanism — primary. Access: Publisher primary abstract, structural Results excerpts and bibliographic identity. Claim fit: RBCC dimer structural assembly model with coiled-coil interactions; no therapy/cure claim or whole-body phase diagnosis. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Viscoelasticity and advective flow of RNA underlies nucleolar form and function — primary. Access: Original PubMed abstract, bibliographic identity and Fig1 descriptions. Claim fit: RNA material organization and nonequilibrium nucleolar flow.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Micropipette aspiration reveals differential RNA-dependent viscoelasticity of nucleolar subcompartments — primary. Access: Consensus fetched primary abstract; Scite primary Results beginning; isolated germinal-vesicle context read. Claim fit: Nucleolar GC more liquid-like than DFC/FC, RNA-sensitive viscoelasticity; extracted Xenopus germinal vesicle, not general intact-cell modulus. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Dynamics of component exchange at PML nuclear bodies — primary. Access: Scite primary abstract + DOI metadata. Claim fit: Distinct PML isoform and partner exchange/retention; not a whole-body liquid phase measurement. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Nuclear body phase separation drives telomere clustering in ALT cancer cells — primary. Access: Official PubMed primary abstract and metadata. Claim fit: Synthetic telomeric condensates test clustering versus ALT synthesis requirements.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention — primary. Access: Publisher primary Results, component FRAP, RNA pulse labeling and selected Discussion. Claim fit: PP1/kinase perturbations alter component exchange and RNA retention in HeLa/hiPSC contexts.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Induced proximity to PML protects TDP-43 from aggregation via SUMO–ubiquitin networks — primary. Access: Publisher primary abstract and Results opening; original PubMed metadata. Claim fit: SUMO2 fusion and engineered PML proximity reduce stress-induced insolubility; p97-dependent pathway.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice — primary. Access: Scite short primary abstract; official PubMed primary abstract. Claim fit: Mouse tissue-selective NEAT1_2/paraspeckles and viable/fertile deficient animals under reported conditions; no universal human physiology conclusion. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Paraspeckle condensation is controlled via TDP-43 polymerization and linked to neuroprotection — primary. Access: Consensus fetched primary abstract; Scite primary main Results beginning. Claim fit: Concentration/polymerization/RNA-binding-dependent paraspeckle regulation; repeat deletion and stressed human-neuron cytoprotection, patient survival association not clinical efficacy. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies — primary. Access: Primary publication abstract and bibliographic record. Claim fit: FRAP-constrained reaction model predicts assembly enhancement and tested SART3–coilin interaction.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells — primary. Access: Scite primary main body introduction and indexed primary result context. Claim fit: Human cell-line chromatin motion/compaction effects make hexanediol sensitivity a nonselective phase-mechanism test. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Scientific text and references appraised at recorded source depth · research
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (4)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary experimental research. Access: Scite primary abstract; root independently read actual PMC5127388 main Results, Fig2E and main Methods on 12 October; supplements not read. Claim fit: Xenopus nucleoli plus NPM1/FIB1/RNA reconstitution, two reconstituted condensed phases and solution, component differences; R=50-nm probe particles in vitro, in-vivo fusion constrains viscosity/surface-tension ratio
Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins — primary experimental research. Access: Scite identity; SciSpace primary abstract; root actual PMC3998805 main Results and Fig2/Fig3 captions. Claim fit: Oxidative PML mesh, subsequent SUMO/SIM partner retention, partner SUMOylation and selected RNF4 degradation; narrow CHO shell/core immuno-EM in Fig3B retained
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Scientific text and references appraised at recorded source depth · research
RNA processing is a newer independently perturbed variable
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (7)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary study. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.
Compositional Control of Phase-Separated Cellular Bodies — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Engineered multivalent scaffold/client partitioning, valency and stoichiometry, with analogous PML/P-body observations; not every endogenous body.
Phase transitions in the assembly of multivalent signalling proteins — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Multivalent demixing with qualified sol–gel interpretation in reconstituted mixtures; not universal nuclear percolation threshold.
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Quinodoz and colleagues mapped rRNA maturation and engineered nucleoli with processing defects. Altered small-subunit processing reordered layers and blocked outward rRNA movement. These experiments connect architecture and substrate maturation in a particular condensate; they do not make FRAP recovery alone a measurement of ribosome-assembly rate, elastic modulus or phase coexistence. Quinodoz et al. (2025) .
Scientific text and references appraised at recorded source depth · research
A third primary example links RNA maturation and compartment structure
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (3)
Compositional Control of Phase-Separated Cellular Bodies — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Engineered multivalent scaffold/client partitioning, valency and stoichiometry, with analogous PML/P-body observations; not every endogenous body.
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Quinodoz and colleagues mapped rRNA maturation by sequencing and imaging and perturbed it in engineered nucleoli. Small-subunit processing defects could reverse layer order and prevent outward rRNA movement. This supplies a nucleolar example in which the RNA substrate helps determine architecture. It complements scaffold-client partitioning and viral-DNA enrichment without making the three mechanisms interchangeable. Quinodoz et al. (2025) .
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: HSV1-associated PolII enrichment consistent with accessible-DNA interactions in defined cells; not universal compartment mechanism.
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Scientific text and references appraised at recorded source depth · research
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (7)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary experimental research. Access: Scite primary abstract; root independently read actual PMC5127388 main Results, Fig2E and main Methods on 12 October; supplements not read. Claim fit: Xenopus nucleoli plus NPM1/FIB1/RNA reconstitution, two reconstituted condensed phases and solution, component differences; R=50-nm probe particles in vitro, in-vivo fusion constrains viscosity/surface-tension ratio
Compositional Control of Phase-Separated Cellular Bodies — primary experimental research. Access: Scite primary abstract; actual PMC4967043 main Results, scaffold/client comparisons, Fig1–5 descriptions. Claim fit: Specific client binding, scaffold stoichiometry/valency, selective partitioning and different component recovery; model systems do not diagnose all bodies
Phase transitions in the assembly of multivalent signalling proteins — primary experimental research. Access: Scite primary Methods summary and figure captions plus qualified discussion excerpt; abstract identity. Claim fit: SH3/PRM, PTB/RNA and nephrin systems; valency-dependent demixing and qualified sol–gel coupling; no universal endogenous phase diagnosis
Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins — primary experimental research. Access: Scite identity; SciSpace primary abstract; root actual PMC3998805 main Results and Fig2/Fig3 captions. Claim fit: Oxidative PML mesh, subsequent SUMO/SIM partner retention, partner SUMOylation and selected RNF4 degradation; narrow CHO shell/core immuno-EM in Fig3B retained
Nuclear speckles enable processing of RNA from GC-rich isochores — primary experimental research. Access: Consensus fetched identity; SciSpace and PubMed primary abstract; actual PMC13283296 selected main Results/Fig1–4 captions. Claim fit: Acute SON/SRRM2 loss in human cells affects short GC-rich intron processing and accumulated RNA more than nascent RNA; protein loss and architecture remain coupled
1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells — primary experimental research. Access: Scite primary main body introduction and indexed primary result context. Claim fit: Human cell-line chromatin motion/compaction effects make hexanediol sensitivity a nonselective phase-mechanism test
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Scientific text and references appraised at recorded source depth · research
A newer force experiment preserves the preparation boundary
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (6)
Heterogeneous force response of chromatin in isolated nuclei. — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Bergamaschi and colleagues combined optical-tweezer deformation of isolated nuclei with fluorescence imaging. Chromatin deformed more readily than the nuclear envelope below the reported 30% strain regime, and nuclease treatment softened nuclei. These measurements help resolve component contributions in that preparation. They do not turn a nuclear-shape change in a patient image into a calibrated mechanical measurement or a disease prognosis. Bergamaschi et al. (2024) .
Nuclear envelope rupture and repair during cancer cell migration — primary study. Access: Primary author-manuscript main Abstract/Results pages1–4 and Figures1/2/4; supplementary Methods and raw data not reanalysed.. Claim fit: NLS-reporter rupture, defined in-vitro and mouse-dermis models, deformation-associated damage foci and ESCRT-III-dependent resealing independently match primary main Results/Figures. Mixed-topic Scite opening excluded.
Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction — primary study. Access: Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.. Claim fit: LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Mitochondria-derived nuclear ATP surge protects against confinement-induced proliferation defects — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: The Ghose et al. (2025) reported mitochondrial repositioning toward the nuclear periphery and a nuclear ATP rise sensitive to mitochondrial ATP production and actin organization. This offers a mitochondria-associated route alongside the stimulus-specific NUDIX5 route above. It does not establish that one source supplies most ATP in every nuclear compartment. Ghose et al. (2025) .
Nuclear position and local acetyl-CoA production regulate chromatin state — primary study. Access: Bibliographic metadata and primary abstract via SciSpace/discovery where available; full-text retrieval failed after Scite quota.. Claim fit: A Willnow and Teleman (2024) linked nuclear position near the epithelial surface with increased acetyl-CoA synthase and histone acetylation. Fatty-acid oxidation contributed to that tissue pattern. These spatial and metabolic perturbations provide a defined tissue context; they do not establish an autonomous metabolic circuit in every nucleus. Willnow and Teleman (2024) .
ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: ACLY-associated cellular carbon supply/histone acetylation in mammalian models; no autonomous nuclear metabolic circuit.
This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies.
Sources and access depth (14)
Optical Measurements of Frequency-Dependent Linear Viscoelastic Moduli of Complex Fluids — primary. Access: Primary citation identity and primary abstract through author/index record; complete experimental text not read.. Claim fit: Thermal probe fluctuations related to linear viscoelastic response in tested complex fluids; extrapolation to actively driven nuclei requires additional assumptions.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Mapping eGFP Oligomer Mobility in Living Cell Nuclei — primary. Access: Primary PLOS main Abstract, Methods data analysis/acquisition/calibration and selected Results/Discussion; no raw data reanalysis.. Claim fit: eGFP oligomer FCS outside nucleoli: calibrated two-normal-diffusion components plus triplet term; cell/model/probe constraints retained.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force — primary. Access: Primary manuscript main Summary, Results on microrheology and mechanomemory, Figures 1–5 and Discussion read; supplemental figures and raw measurements not reanalysed.. Claim fit: 200-nm-diameter targeted magnetic particles in CHO DHFR reporter nuclei; 0.1–5 Hz force response and separate hiPSC Pol II arm; local perturbation and injection limitations.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology — primary. Access: Root independently read primary PMC12173521 Abstract and selected main Methods/Results paragraphs, including oscillatory preparation, hydrodynamic drag correction, morphology and Jeffreys analysis; primary Scite webpage identity corroborated. Supplement and raw-data reanalysis excluded.. Claim fit: Oscillatory AFM on live and isolated MCF7 nuclei, hydrodynamic-drag validation, modulus/loss-tangent distinction and Jeffreys model. The published author list supersedes incomplete Consensus authors.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1 — primary. Access: Published PDF front matter, main preparation/treatment Methods, Results around Figure 9 and Discussion read; supplementary data not appraised.. Claim fit: Metabolically active karyoplast compression/dissipation and BRM-014 inhibition; BRM-014 inhibits BRM and BRG1, so pharmacology is not exclusive genetic proof for BRG1. Karyoplasts are not bare detergent-isolated nuclei.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Heterogeneous force response of chromatin in isolated nuclei. — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Bergamaschi and colleagues measured isolated-nucleus force responses together with chromatin and nuclear-envelope deformation. Chromatin was more compliant than the envelope below the reported 30% strain regime, and chromatin digestion softened nuclei. The joint readouts strengthen component interpretation in the tested preparation without defining one elastic modulus or viscosity for every nucleus. Bergamaschi et al. (2024) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility — primary. Access: Published identity and primary abstract from author-manuscript repository; full main text not appraised.. Claim fit: Differently sized inert GFP probes and polymer simulations; size-dependent intermediate-scale viscoelastic behavior and obstacle-network model; not universal fixed fractal organization.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Fluid Mechanics of Microrheology — seminal review. Access: Publisher bibliographic identity and abstract; established mathematical relationships independently checked dimensionally. Detailed review body not appraised.. Claim fit: Foundational synthesis of probe/bulk coupling, passive thermal-fluctuation and active-force microrheology assumptions; not a nuclear measurement.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Robust model-based analysis of single-particle tracking experiments with Spot-On — primary. Access: Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.. Claim fit: Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Reaction-diffusion FRAP solutions constrain binding inference; not every recovery curve identifies every parameter.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Attar and colleagues used polymer simulations compared with micromechanical and chromosome-contact measurements. In that model, peripheral chromatin attachment transmitted imposed nuclear forces to chromatin, and internal crosslinks stiffened the nucleus only when that peripheral coupling was present. This is a model-constrained account of load transfer; a mapped lamina association by itself does not establish the strength or permanence of every molecular tether. Attar et al. (2025) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies.
Sources and access depth (19)
Architecture of the linker-scaffold in the nuclear pore — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Linker/scaffold structural integration and flexible ring-spoke models; model architecture not universal transport threshold.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Architecture of the cytoplasmic face of the nuclear pore — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Composite human/fungal cytoplasmic-face architecture and approximate composition; not one atomic image of a functioning pore.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Simple rules for passive diffusion through the nuclear pore complex — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Ran-system asymmetry regulates particular import/export reporters; not all cargo uses the same energy mechanism.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Nuclear pore permeability and fluid flow are modulated by its dilation state — primary. Access: Consensus fetched primary record and search-returned primary abstract; full Results inaccessible. Online 2024; issue year should not replace online publication date.. Claim fit: Dictyostelium osmotic adaptation, dilation-dependent pressure-driven nucleocytosolic fluid flow and viral blockage; not identical to diffusion or receptor-driven transport.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Visualizing nuclear pore complex plasticity with pan-expansion microscopy — primary. Access: Fetched primary abstract and publication record; full Methods and Results not yet appraised.. Claim fit: Expanded fixed-cell NPC diameter distributions, nuclear-surface bias, hyperosmotic constriction and LINC perturbation; one patient-derived neuronal comparison does not establish all ALS.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Karyopherins remodel the dynamic organization of the nuclear pore complex transport barrier — primary. Access: Publisher primary Abstract, opening Results on isolated yeast NPCs, selected DNA-origami Results and Discussion read; entire Methods and supplements not appraised.. Claim fit: High-speed AFM of isolated yeast NPCs and orthogonal approaches; transport-factor-dependent FG organization, mobile central cluster, altered FG mutants, and contrast with hydrogels.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Structure and gating of the nuclear pore complex — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Xenopus oocyte NPC cryo-tomographic scaffold/channel structure; not direct universal transport kinetics.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
The HIV capsid mimics karyopherin engagement of FG-nucleoporins — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: The Dickson et al. (2024) used an in-vitro dissection of the nuclear barrier and identified a capsid pocket engaging FG motifs from several nucleoporins. Capsids penetrated tested FG condensates, supporting a karyopherin-mimicry interpretation for a large viral cargo. This illustrates why interaction chemistry matters alongside size. Reconstituted-condensate entry is not identical to passage kinetics through an intact, mechanically changing NPC in a living human cell. Dickson et al. (2024) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Cell type‐specific nuclear pores: a case in point for context‐dependent stoichiometry of molecular machines — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: NPC stoichiometry comparisons across human cell lines and calibrated counting; no invariant universal composition.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Long-lived scaffold components and age-associated permeability loss in defined postmitotic models; not all human ageing or every NPC component.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Characterisation of the passive permeability barrier of nuclear pore complexes — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Probe passage in permeabilized nuclei and barrier perturbations; distinct from living-yeast passive exchange.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Correlative main-text interphase NPC membrane intermediates; not a full mitotic assembly account.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
ESCRT-III controls nuclear envelope reformation — primary. Access: Fetched primary abstract and identity; full Methods not accessible.. Claim fit: CHMP2A/CHMP4B/UFD1-dependent postmitotic envelope sealing and compartmentalization in human cells, not all envelope-repair routes.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
LEM2 phase separation governs ESCRT-mediated nuclear envelope reformation — primary. Access: Fetched primary abstract and identity plus selected primary Results excerpts; complete Methods/supplements not appraised.. Claim fit: LEM2 chromatin/microtubule targeting and CHMP7 activation in postmitotic reformation; O-ring is mechanistic model, not every membrane-less-body mechanism.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores — primary. Access: Publisher primary selected Results on force application and import/export plus AFM Methods excerpt read; complete body and supplements not appraised.. Claim fit: Force-dependent YAP entry in defined fibroblast/MCF10A systems, nuclear deformation and import-rate assays; not all cargo or universal pore-mechanics explanation.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes — primary. Access: Fetched primary abstract and publisher Results excerpts on Xenopus assembly and density model; Crossmark publication date and author metadata checked. Complete body and supplements not appraised.. Claim fit: Nuclear/cytoplasmic density differences and pressure-balance model constrained by transport, chromatin and embryo observations. Erroneous2023 provider year corrected to publisher15August2025.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Nuclear envelope rupture and repair during cancer cell migration — primary. Access: Primary author-manuscript main Abstract/Results pages1–4 and Figures1/2/4; supplementary Methods and raw data not reanalysed.. Claim fit: NLS-reporter rupture, defined in-vitro and mouse-dermis models, deformation-associated damage foci and ESCRT-III-dependent resealing independently match primary main Results/Figures. Mixed-topic Scite opening excluded.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Scientific text and references appraised at recorded source depth · research
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (3)
SON and SRRM2 are essential for nuclear speckle formation — primary experimental research. Access: Scite main body and targeted primary Results/figure excerpts. Claim fit: SON/SRRM2 combination disperses speckle proteins in HAP1/HEK293 models; monoclonal SC35 principal speckle target is SRRM2, historic SRSF2 attribution inappropriate
Nuclear speckles enable processing of RNA from GC-rich isochores — primary experimental research. Access: Consensus fetched identity; SciSpace and PubMed primary abstract; actual PMC13283296 selected main Results/Fig1–4 captions. Claim fit: Acute SON/SRRM2 loss in human cells affects short GC-rich intron processing and accumulated RNA more than nascent RNA; protein loss and architecture remain coupled
Gene expression amplification by nuclear speckle association — primary experimental research. Access: Scite primary abstract; PubMed identity and selected primary figure context. Claim fit: Heat-shock Hsp70/HSPA1B RNA accumulation/proximity in human and hamster systems, reduced degradation contribution; not a pure initiation or splicing-rate measure
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Scientific text and references appraised at recorded source depth · research
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (4)
SON and SRRM2 are essential for nuclear speckle formation — primary experimental research. Access: Scite main body and targeted primary Results/figure excerpts. Claim fit: SON/SRRM2 combination disperses speckle proteins in HAP1/HEK293 models; monoclonal SC35 principal speckle target is SRRM2, historic SRSF2 attribution inappropriate
Nuclear speckles enable processing of RNA from GC-rich isochores — primary experimental research. Access: Consensus fetched identity; SciSpace and PubMed primary abstract; actual PMC13283296 selected main Results/Fig1–4 captions. Claim fit: Acute SON/SRRM2 loss in human cells affects short GC-rich intron processing and accumulated RNA more than nascent RNA; protein loss and architecture remain coupled
Gene expression amplification by nuclear speckle association — primary experimental research. Access: Scite primary abstract; PubMed identity and selected primary figure context. Claim fit: Heat-shock Hsp70/HSPA1B RNA accumulation/proximity in human and hamster systems, reduced degradation contribution; not a pure initiation or splicing-rate measure
SRRM2 phase separation drives assembly of nuclear speckle subcompartments — primary experimental research. Access: Consensus fetched identity + search primary abstract; SciSpace exact primary abstract + Scite identity; reader had no text. Claim fit: SRRM2/SON subcompartments, distinct target subsets and attributed coacervation mechanism; no universal phase-only splicing necessity
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
This scholarly synthesis integrates foundational studies and literature available by 12 October 2026. Source access ranges from primary abstracts to selected Results, figure captions and Methods, as specified for each reference. Experiments and models retain their organism, construct and perturbation context; raw data and supplementary material have not been comprehensively reanalysed.
Sources and access depth (14)
SON and SRRM2 are essential for nuclear speckle formation — primary. Access: Scite main body and targeted primary Results/figure excerpts. Claim fit: SON/SRRM2 combination disperses speckle proteins in HAP1/HEK293 models; monoclonal SC35 principal speckle target is SRRM2, historic SRSF2 attribution inappropriate. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Genome organization around nuclear speckles drives mRNA splicing efficiency — primary. Access: Consensus fetched primary abstract; publisher abstract and figure-caption descriptions. Claim fit: Speckle-proximal spliceosome binding and splicing; directed RNA recruitment tests spatial sufficiency.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Nuclear speckles enable processing of RNA from GC-rich isochores — primary. Access: Consensus fetched identity; SciSpace and PubMed primary abstract; actual PMC13283296 selected main Results/Fig1–4 captions. Claim fit: Acute SON/SRRM2 loss in human cells affects short GC-rich intron processing and accumulated RNA more than nascent RNA; protein loss and architecture remain coupled. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
RNA localization to nuclear speckles follows splicing logic — primary. Access: Consensus fetched primary abstract and DOI/author/year record. Claim fit: Sequence-dependent localization, early spliceosome interactions and splicing-competent construct kinetics.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention — primary. Access: Publisher primary Results, component FRAP, RNA pulse labeling and selected Discussion. Claim fit: PP1/kinase perturbations alter component exchange and RNA retention in HeLa/hiPSC contexts.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Nuclear speckles — seminal review. Access: Primary publication abstract and bibliographic record. Claim fit: Foundational definitions, interchromatin granule cluster identity and RNA-processing context.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Gene expression amplification by nuclear speckle association — primary. Access: Scite primary abstract; PubMed identity and selected primary figure context. Claim fit: Heat-shock Hsp70/HSPA1B RNA accumulation/proximity in human and hamster systems, reduced degradation contribution; not a pure initiation or splicing-rate measure. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
SRRM2 phase separation drives assembly of nuclear speckle subcompartments — primary. Access: Consensus fetched identity + search primary abstract; SciSpace exact primary abstract + Scite identity; reader had no text. Claim fit: SRRM2/SON subcompartments, distinct target subsets and attributed coacervation mechanism; no universal phase-only splicing necessity. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Malat1 is not an essential component of nuclear speckles in mice — primary. Access: Primary publication abstract and bibliographic record. Claim fit: Viable fertile knockout mice with retained marker localization under laboratory conditions; contextual necessity.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
RBBP6 anchors pre-mRNA 3′ end processing to nuclear speckles for efficient gene expression — primary. Access: Root browser independently read actual PMC main Results, Fig1–6 captions, limitations and selected Methods; supplements and raw data not appraised. Claim fit: Domain-rescue experiments distinguish catalytic NTD from IDR4-supported spatial recruitment; APA/readthrough and RNA-localization outcomes retain model/assay context.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies.
Sources and access depth (16)
Mapping eGFP Oligomer Mobility in Living Cell Nuclei — primary. Access: Primary PLOS main Abstract, Methods data analysis/acquisition/calibration and selected Results/Discussion; no raw data reanalysis.. Claim fit: eGFP oligomer FCS outside nucleoli: calibrated two-normal-diffusion components plus triplet term; cell/model/probe constraints retained.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility — primary. Access: Published identity and primary abstract from author-manuscript repository; full main text not appraised.. Claim fit: Differently sized inert GFP probes and polymer simulations; size-dependent intermediate-scale viscoelastic behavior and obstacle-network model; not universal fixed fractal organization.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force — primary. Access: Primary manuscript main Summary, Results on microrheology and mechanomemory, Figures 1–5 and Discussion read; supplemental figures and raw measurements not reanalysed.. Claim fit: 200-nm-diameter targeted magnetic particles in CHO DHFR reporter nuclei; 0.1–5 Hz force response and separate hiPSC Pol II arm; local perturbation and injection limitations.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology — primary. Access: Root independently read primary PMC12173521 Abstract and selected main Methods/Results paragraphs, including oscillatory preparation, hydrodynamic drag correction, morphology and Jeffreys analysis; primary Scite webpage identity corroborated. Supplement and raw-data reanalysis excluded.. Claim fit: Oscillatory AFM on live and isolated MCF7 nuclei, hydrodynamic-drag validation, modulus/loss-tangent distinction and Jeffreys model. The published author list supersedes incomplete Consensus authors.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1 — primary. Access: Published PDF front matter, main preparation/treatment Methods, Results around Figure 9 and Discussion read; supplementary data not appraised.. Claim fit: Metabolically active karyoplast compression/dissipation and BRM-014 inhibition; BRM-014 inhibits BRM and BRG1, so pharmacology is not exclusive genetic proof for BRG1. Karyoplasts are not bare detergent-isolated nuclei.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Heterogeneous force response of chromatin in isolated nuclei. — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Bergamaschi and colleagues measured isolated-nucleus force responses together with chromatin and nuclear-envelope deformation. Chromatin was more compliant than the envelope below the reported 30% strain regime, and chromatin digestion softened nuclei. The joint readouts strengthen component interpretation in the tested preparation without defining one elastic modulus or viscosity for every nucleus. Bergamaschi et al. (2024) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Fluid Mechanics of Microrheology — seminal review. Access: Publisher bibliographic identity and abstract; established mathematical relationships independently checked dimensionally. Detailed review body not appraised.. Claim fit: Foundational synthesis of probe/bulk coupling, passive thermal-fluctuation and active-force microrheology assumptions; not a nuclear measurement.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Optical Measurements of Frequency-Dependent Linear Viscoelastic Moduli of Complex Fluids — primary. Access: Primary citation identity and primary abstract through author/index record; complete experimental text not read.. Claim fit: Thermal probe fluctuations related to linear viscoelastic response in tested complex fluids; extrapolation to actively driven nuclei requires additional assumptions.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Reaction-diffusion FRAP solutions constrain binding inference; not every recovery curve identifies every parameter.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Robust model-based analysis of single-particle tracking experiments with Spot-On — primary. Access: Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.. Claim fit: Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
A Molecular Sensor Reveals Differences in Macromolecular Crowding between the Cytoplasm and Nucleoplasm — primary. Access: Publisher primary abstract, author metadata and list of supplemental controls; complete Results not accessible. Journal article distinguished from same-title conference abstract.. Claim fit: Oligonucleotide FRET sensor, in-vitro crowder responses and compartment/perturbation contrasts; signal reflects calibrated sensor behavior rather than universal mass density.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes — primary. Access: Fetched primary abstract and publisher Results excerpts on Xenopus assembly and density model; Crossmark publication date and author metadata checked. Complete body and supplements not appraised.. Claim fit: Nuclear/cytoplasmic density differences and pressure-balance model constrained by transport, chromatin and embryo observations. Erroneous2023 provider year corrected to publisher15August2025.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
A sensor for quantification of macromolecular crowding in living cells — primary. Access: Fetched primary abstract and identity; full methods not read.. Claim fit: Genetically encoded FRET crowding sensor in bacterial and mammalian cells; assay principle does not supply nuclear-specific values.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Scientific text and references appraised at recorded source depth · research
Processing-associated architecture differs from a p53 readout
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (3)
The 5S RNP Couples p53 Homeostasis to Ribosome Biogenesis and Nucleolar Stress — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: 5S RNP/RPL5/RPL11 regulation of MDM2 and p53 under defined ribosome-biogenesis perturbations; not all stress pathways.
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Quinodoz and colleagues experimentally linked rRNA processing defects to altered nucleolar layer order and impaired rRNA outflux. This supplies a recent structural/processing endpoint, distinct from the MDM2–p53 abundance endpoints in the earlier studies. A reorganized nucleolus is therefore not a quantitative measure of p53 activation, and this newer study should not be used alone to assign a stress-checkpoint mechanism. Quinodoz et al. (2025) .
This scholarly synthesis integrates foundational studies and literature available by 12 October 2026. Source access ranges from primary abstracts to selected Results, figure captions and Methods, as specified for each reference. Experiments and models retain their organism, construct and perturbation context; raw data and supplementary material have not been comprehensively reanalysed.
Sources and access depth (9)
The nucleolus as a multiphase liquid condensate — seminal review. Access: Publisher and PubMed abstract and selected definition/context excerpts. Claim fit: Foundational synthesis of ribosome biogenesis and nucleolar compartments; online2020, issue2021.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary. Access: Scite primary abstract; root independently read actual PMC5127388 main Results, Fig2E and main Methods on 12 October; supplements not read. Claim fit: Xenopus nucleoli plus NPM1/FIB1/RNA reconstitution, two reconstituted condensed phases and solution, component differences; R=50-nm probe particles in vitro, in-vivo fusion constrains viscosity/surface-tension ratio. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Viscoelasticity and advective flow of RNA underlies nucleolar form and function — primary. Access: Original PubMed abstract, bibliographic identity and Fig1 descriptions. Claim fit: RNA material organization and nonequilibrium nucleolar flow.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary. Access: Consensus fetched primary abstract + Scite metadata; no full body retrieved. Claim fit: Spatial rRNA maturation and synthetic nucleolar organization; RNA as scaffold/substrate, not architecture-only function. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Micropipette aspiration reveals differential RNA-dependent viscoelasticity of nucleolar subcompartments — primary. Access: Consensus fetched primary abstract; Scite primary Results beginning; isolated germinal-vesicle context read. Claim fit: Nucleolar GC more liquid-like than DFC/FC, RNA-sensitive viscoelasticity; extracted Xenopus germinal vesicle, not general intact-cell modulus. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress — primary. Access: Original PMC Summary and selected MDM2/5S RNA interaction Results. Claim fit: 5S RNP-mediated connection between ribosome biogenesis and p53 regulation.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Scientific text and references appraised at recorded source depth · research
PARP-dependent turnover and recruitment can lead to different endpoints
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (5)
Poly(ADP-ribosyl)ation of TIMELESS limits DNA replication stress and promotes stalled fork protection — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Rageul and colleagues linked TIMELESS PARylation to proteasomal turnover. A PARylation-refractory TIMELESS mutant or PARP inhibition caused excessive fork-associated TIMELESS and impaired RAD51-associated protection in their stressed cell models. The result concerns regulated replisome remodeling, rather than a universal rule that more PAR always produces better repair. Rageul et al. (2024) .
HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: HPF1/PARP composite active site and serine modification supported by biochemical/structural cellular comparisons; no universal chain assignment.
XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Lin and colleagues found that XRCC1 supported PARP1/PAR-dependent PARP2 recruitment, while its loss increased PARP1 activation and reduced PARP2 foci. Sensor recruitment and PAR amount therefore need separate interpretation; the observation is not a universal chain-length assignment for PARP1 versus PARP2. Lin et al. (2025) .
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
This scholarly synthesis integrates foundational studies and literature available by 12 October 2026. Source access ranges from primary abstracts to selected Results, figure captions and Methods, as specified for each reference. Experiments and models retain their organism, construct and perturbation context; raw data and supplementary material have not been comprehensively reanalysed.
Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies — primary. Access: Scite primary main body and targeted Results/figure/Discussion excerpts. Claim fit: HeLa/NIH3T3 prepared-section RNA/protein EM localization; terminal/core organization, cross-wise versus looped alternative unresolved; not cryo-ET or kinetic evidence. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice — primary. Access: Scite short primary abstract; official PubMed primary abstract. Claim fit: Mouse tissue-selective NEAT1_2/paraspeckles and viable/fertile deficient animals under reported conditions; no universal human physiology conclusion. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Paraspeckle condensation is controlled via TDP-43 polymerization and linked to neuroprotection — primary. Access: Consensus fetched primary abstract; Scite primary main Results beginning. Claim fit: Concentration/polymerization/RNA-binding-dependent paraspeckle regulation; repeat deletion and stressed human-neuron cytoprotection, patient survival association not clinical efficacy. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body — primary. Access: Consensus fetched primary abstract; Scite primary introduction/Results beginning. Claim fit: Multi-positional NEAT1 labeling, morphological sorting and 3D STED ensemble architecture; no direct live material-state/atomic structure. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Paraspeckles are constructed as block copolymer micelles — primary. Access: Scite primary abstract. Claim fit: RNA-domain deletion/transcription comparisons plus explicitly proposed micellization model. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Regulating gene expression through RNA nuclear retention — primary. Access: Primary publication abstract and bibliographic record. Claim fit: Mouse CTN-RNA nuclear retention, paraspeckle association and stress-dependent processing to mCAT2 coding RNA.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Scientific text and references appraised at recorded source depth · research
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Sources and access depth (7)
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary experimental research. Access: Scite primary abstract; root independently read actual PMC5127388 main Results, Fig2E and main Methods on 12 October; supplements not read. Claim fit: Xenopus nucleoli plus NPM1/FIB1/RNA reconstitution, two reconstituted condensed phases and solution, component differences; R=50-nm probe particles in vitro, in-vivo fusion constrains viscosity/surface-tension ratio
Compositional Control of Phase-Separated Cellular Bodies — primary experimental research. Access: Scite primary abstract; actual PMC4967043 main Results, scaffold/client comparisons, Fig1–5 descriptions. Claim fit: Specific client binding, scaffold stoichiometry/valency, selective partitioning and different component recovery; model systems do not diagnose all bodies
Phase transitions in the assembly of multivalent signalling proteins — primary experimental research. Access: Scite primary Methods summary and figure captions plus qualified discussion excerpt; abstract identity. Claim fit: SH3/PRM, PTB/RNA and nephrin systems; valency-dependent demixing and qualified sol–gel coupling; no universal endogenous phase diagnosis
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (6)
10.1073/pnas.1302950110 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1016/j.cell.2019.08.037 — primary research. Access: indexed primary results discussion plus root browser results figures2 5 7. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite provided Highlights; Consensus fetch supplied only a takeaway, which was not used as evidence. Indexed primary PMC Results/Discussion inspected. Root independently opened actualPMC6778041 ResultsP18+Fig2whole/partialFRAP, P32+Fig5p300/AcetylCoA recruitment-dependent dissolution, and P39+Fig7acetylchromatin/reader multivalency. MainResults and captions support retained fusion/exchange/acetylation/reader observations; supplements/rawdata not reanalyzed.
10.1016/j.molcel.2020.02.005 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.15252/embj.2020107270 — primary research. Access: primary abstract. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.7554/eLife.30294 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
HP1 loses its chromatin clustering and phase separation function across evolution — primary experiment. Access: Consensus fetched primary abstract and official publisher abstract and selected Results inspected. Scite had metadata but no readable body.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Nucleotide Deficiency Promotes Genomic Instability in Early Stages of Cancer Development — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Nucleotide insufficiency, replication perturbation and rescue in oncogene-transformed cell models; not universal human-cancer initiation.
Poly(ADP-ribosyl)ation of TIMELESS limits DNA replication stress and promotes stalled fork protection — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Rageul and colleagues reported that PARylation-related TIMELESS turnover limited abnormal helicase engagement and supported RAD51 loading in stalled-fork models. Preventing this turnover sensitized BRCA2-deficient cells to replication-associated damage. This identifies another experimentally defined route to fork instability; it does not equate cell-model sensitivity with patient benefit or replace a direct test of homologous-recombination repair. Rageul et al. (2024) .
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Cell correction content and possible conclusion impact remain unverified, explicitly disclosed on the page.
Every retained reference identity and attributed major-claim fit appraised at recorded access depth.
Citation metrics and automated supporting/contrasting classifications were not treated as proof.
Sources and access depth (4)
10.1126/science.1181369 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1038/s41586-019-1778-y — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
10.1126/science.abn6583 — primary research. Access: selected primary body plus root browser results figure3. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected body inspected. Root independently opened actualPMC9069445 ResultsP14/P15 and Figure3D-F, confirming model-inferred median10–30min with censoring correction, distinct mean15–45min; one505kbFbn2G1/earlyS mESCcontext.
Uniform dynamics of cohesin-mediated loop extrusion in living human cells — primary experiment and model. Access: Consensus fetched primary abstract and Scite selected main-text passages, including study design and initial Results; not every supplementary analysis inspected.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
Scientific text and references appraised at recorded source depth · research
RNA maturation can be tested as an architectural variable
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (5)
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Quinodoz and colleagues mapped rRNA processing and used engineered nucleoli to test the relationship between maturation and layer organization. Small-subunit processing defects changed layer order and impeded outward rRNA movement. The nucleolar result illustrates a substrate-linked architectural mechanism; it should not be assigned to paraspeckles or nuclear speckles without their own RNA-processing and perturbation evidence. Quinodoz et al. (2025) .
Gene expression amplification by nuclear speckle association — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Hsp70 speckle association and higher RNA accumulation in defined heat-shock models; intronless genes do not test intron removal.
Paraspeckles are constructed as block copolymer micelles — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: NEAT1-domain perturbations and block-copolymer micelle model for paraspeckles; no every-RNP assembly law.
SON and SRRM2 are essential for nuclear speckle formation — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: SON/SRRM2 perturbations and SC35 reagent identity in defined human models; molecular functions not selectively separated from geometry.
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy — primary study. Access: Bibliographic metadata and primary abstract via SciSpace/discovery where available; full-text retrieval failed after Scite quota.. Claim fit: Rahman and colleagues used labeled nuclear proteins and histone modifications in multiplexed super-resolution fluorescence imaging, rather than inferring their identities from elemental contrast. Their scale-dependent spatial associations illustrate why elemental maps and molecularly targeted fluorescence provide complementary observables. Neither co-distribution nor a localization-precision estimate alone proves a specific molecular contact or the resolution of an entire reconstructed structure. Rahman et al. (2025) .
Scientific text and references appraised at recorded source depth · research
Retained foundational studies have matched DOI/title identities. Study systems and limitations were kept explicit; no FRAP/hexanediol/shape-only phase diagnosis retained.
Recent literature contains both particular functional assembly models and non-demixing explanations. These are not collapsed into one universal verdict.
Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging — primary experimental research. Access: Scite primary main Results including locus identity, controls and distance/inference description. Claim fit: Silent Fbn2 locus in mESCs; distances and Bayesian loop-state inference are separate from live RNA production
A single cluster of RNA Polymerase II molecules is stably associated with active genes — primary experimental research. Access: Consensus fetched record + Scite primary abstract; official publisher main Results/Discussion read. Claim fit: Fly-embryo Pol II clustering explained by engaged-polymerase accumulation with imaging and simulations; ordinary clusters distinct from histone locus bodies; publisher date resolves Consensus 2025 metadata discrepancy
Remaining limits
This is an independent HTML text/reference appraisal at documented abstract, selected-main-text and figure-caption depths, not raw-data reanalysis, a systematic review or whole-package certification.
Associated Word archives, supplements, figure licensing and exhaustive literature coverage remain outside this appraisal.
No absent Scite notice field is treated as proof of no editorial notices.
10.1038/s41467-023-39846-y — primary research. Access: selected primary body and indexed results. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: Scite selected primarybody inspected; indexedPMC10333366Results independently confirm H1e/H3K27me3regional associations, partialH1c/d/e-loss with unchangedSUZ12, restoration/mark/mRNA distinctions. Full supplementalmechanistic validation not reproduced.
10.1126/science.1186777 — primary research. Access: selected primary body passages. Claim fit: fits the attributed specimen/observable-bounded narrative; source-specific caveats retained Limit: First readable Scite primarybodypage or primaryabstract inspected; complete article and supplements not claimed.
The fork protection complex promotes parental histone recycling and epigenetic memory — primary experiment. Access: Consensus fetched primary abstract; Scite Introduction, main-text study summary, Figure 1 caption and initial Results inspected. Supplementary validation and raw data not reanalyzed.. Claim fit: used only for the topic-specific dated addition, with specimen/method/model limits stated inline
Remaining limits
Source access differs across references: primary abstract, selected article-body passages, or inspected publisher Results; see evidence inventory.
Supplements, raw data, full mathematical derivations and linked Word drafts were not independently reanalyzed.
Scite MCP quota prevented further excerpt calls after retrieved metadata/body pages; provider failure was not treated as publication absence.
This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies.
Sources and access depth (23)
Coupling of the nucleus and cytoplasm: role of the LINC complex — primary. Access: Primary abstract and bibliographic identity through author institutional repository; full Methods not appraised.. Claim fit: SUN1/SUN2–nesprin2 localization and depletion/overexpression in HeLa cells, perinuclear spacing and LINC model.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Structure and gating of the nuclear pore complex — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Xenopus oocyte NPC cryo-tomographic scaffold/channel structure; not direct universal transport kinetics.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Ran-system asymmetry regulates particular import/export reporters; not all cargo uses the same energy mechanism.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Correlative main-text interphase NPC membrane intermediates; not a full mitotic assembly account.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
ESCRT-III controls nuclear envelope reformation — primary. Access: Fetched primary abstract and identity; full Methods not accessible.. Claim fit: CHMP2A/CHMP4B/UFD1-dependent postmitotic envelope sealing and compartmentalization in human cells, not all envelope-repair routes.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Nuclear envelope rupture and repair during cancer cell migration — primary. Access: Primary author-manuscript main Abstract/Results pages1–4 and Figures1/2/4; supplementary Methods and raw data not reanalysed.. Claim fit: NLS-reporter rupture, defined in-vitro and mouse-dermis models, deformation-associated damage foci and ESCRT-III-dependent resealing independently match primary main Results/Figures. Mixed-topic Scite opening excluded.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis — primary. Access: Publisher primary Abstract and main Results through heterochromatin-tether deconvolution, membrane LAP2 rescue and short/long-term transcription effects read; complete Methods and supplements not appraised. Published 24 February 2026.. Claim fit: Redundant LBR/membrane LAP2 tethering in mammalian cell models, distinction between short-term release and persistent loss; not universal instant repression by peripheral position.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Visualizing nuclear pore complex plasticity with pan-expansion microscopy — primary. Access: Fetched primary abstract and publication record; full Methods and Results not yet appraised.. Claim fit: Expanded fixed-cell NPC diameter distributions, nuclear-surface bias, hyperosmotic constriction and LINC perturbation; one patient-derived neuronal comparison does not establish all ALS.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Nuclear pore permeability and fluid flow are modulated by its dilation state — primary. Access: Consensus fetched primary record and search-returned primary abstract; full Results inaccessible. Online 2024; issue year should not replace online publication date.. Claim fit: Dictyostelium osmotic adaptation, dilation-dependent pressure-driven nucleocytosolic fluid flow and viral blockage; not identical to diffusion or receptor-driven transport.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Attar and colleagues used polymer simulations compared with micromechanical and chromosome-contact measurements. In that model, peripheral chromatin attachment transmitted imposed nuclear forces to chromatin, and internal crosslinks stiffened the nucleus only when that peripheral coupling was present. This is a model-constrained account of load transfer; a mapped lamina association by itself does not establish the strength or permanence of every molecular tether. Attar et al. (2025) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes — primary. Access: Fetched primary abstract and publisher Results excerpts on Xenopus assembly and density model; Crossmark publication date and author metadata checked. Complete body and supplements not appraised.. Claim fit: Nuclear/cytoplasmic density differences and pressure-balance model constrained by transport, chromatin and embryo observations. Erroneous2023 provider year corrected to publisher15August2025.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
The molecular architecture of lamins in somatic cells — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Prepared vimentin-null mouse-fibroblast lamina filament structure; approximately3.5nm filaments are not live-lamina thickness.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Architecture of the linker-scaffold in the nuclear pore — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Linker/scaffold structural integration and flexible ring-spoke models; model architecture not universal transport threshold.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Simple rules for passive diffusion through the nuclear pore complex — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Characterisation of the passive permeability barrier of nuclear pore complexes — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Probe passage in permeabilized nuclei and barrier perturbations; distinct from living-yeast passive exchange.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Architecture of the cytoplasmic face of the nuclear pore — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Composite human/fungal cytoplasmic-face architecture and approximate composition; not one atomic image of a functioning pore.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
LEM2 phase separation governs ESCRT-mediated nuclear envelope reformation — primary. Access: Fetched primary abstract and identity plus selected primary Results excerpts; complete Methods/supplements not appraised.. Claim fit: LEM2 chromatin/microtubule targeting and CHMP7 activation in postmitotic reformation; O-ring is mechanistic model, not every membrane-less-body mechanism.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: LAD association map, domain scales and low expression in human fibroblasts; no universal permanent tether or repression causality.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions — editorial notice. Access: Primary correction abstract/citation record containing full correction statements; original full Methods not reappraised.. Claim fit: Official corrected H3K9me3 identity and Methods data sources; no inferred change to uncorrected abstract-level LAD conclusions.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction — primary. Access: Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.. Claim fit: LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Long-lived scaffold components and age-associated permeability loss in defined postmitotic models; not all human ageing or every NPC component.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies.
Sources and access depth (15)
The molecular architecture of lamins in somatic cells — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Prepared vimentin-null mouse-fibroblast lamina filament structure; approximately3.5nm filaments are not live-lamina thickness.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: LAD association map, domain scales and low expression in human fibroblasts; no universal permanent tether or repression causality.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Mutations in the gene encoding lamin A/C cause autosomal dominant Emery-Dreifuss muscular dystrophy — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Four LMNA variants co-segregated with EDMD in five families; genetics alone does not identify one mechanical defect.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Recurrent de novo point mutations in lamin A cause Hutchinson–Gilford progeria syndrome — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Recurrent G608G in18/20 classical HGPS cases, cryptic splice consequence and50-amino-acid deletion; not ordinary-ageing equivalence.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis — primary. Access: Publisher primary Abstract and main Results through heterochromatin-tether deconvolution, membrane LAP2 rescue and short/long-term transcription effects read; complete Methods and supplements not appraised. Published 24 February 2026.. Claim fit: Redundant LBR/membrane LAP2 tethering in mammalian cell models, distinction between short-term release and persistent loss; not universal instant repression by peripheral position.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Attar and colleagues used polymer simulations compared with micromechanical and chromosome-contact measurements. In that model, peripheral chromatin attachment transmitted imposed nuclear forces to chromatin, and internal crosslinks stiffened the nucleus only when that peripheral coupling was present. This is a model-constrained account of load transfer; a mapped lamina association by itself does not establish the strength or permanence of every molecular tether. Attar et al. (2025) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction — primary. Access: Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.. Claim fit: LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Lamin B1 loss is a senescence-associated biomarker — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: LaminB1 decrease in defined fibroblast senescence states and irradiated-mouse tissue; no standalone individual-cell diagnosis or ordinary ageing equivalence.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Coupling of the nucleus and cytoplasm: role of the LINC complex — primary. Access: Primary abstract and bibliographic identity through author institutional repository; full Methods not appraised.. Claim fit: SUN1/SUN2–nesprin2 localization and depletion/overexpression in HeLa cells, perinuclear spacing and LINC model.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions — editorial notice. Access: Primary correction abstract/citation record containing full correction statements; original full Methods not reappraised.. Claim fit: Official corrected H3K9me3 identity and Methods data sources; no inferred change to uncorrected abstract-level LAD conclusions.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Heterogeneous force response of chromatin in isolated nuclei. — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Bergamaschi and colleagues measured isolated-nucleus force responses together with chromatin and nuclear-envelope deformation. Chromatin was more compliant than the envelope below the reported 30% strain regime, and chromatin digestion softened nuclei. The joint readouts strengthen component interpretation in the tested preparation without defining one elastic modulus or viscosity for every nucleus. Bergamaschi et al. (2024) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1 — primary. Access: Published PDF front matter, main preparation/treatment Methods, Results around Figure 9 and Discussion read; supplementary data not appraised.. Claim fit: Metabolically active karyoplast compression/dissipation and BRM-014 inhibition; BRM-014 inhibits BRM and BRG1, so pharmacology is not exclusive genetic proof for BRG1. Karyoplasts are not bare detergent-isolated nuclei.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology — primary. Access: Root independently read primary PMC12173521 Abstract and selected main Methods/Results paragraphs, including oscillatory preparation, hydrodynamic drag correction, morphology and Jeffreys analysis; primary Scite webpage identity corroborated. Supplement and raw-data reanalysis excluded.. Claim fit: Oscillatory AFM on live and isolated MCF7 nuclei, hydrodynamic-drag validation, modulus/loss-tangent distinction and Jeffreys model. The published author list supersedes incomplete Consensus authors.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Nuclear envelope rupture and repair during cancer cell migration — primary. Access: Primary author-manuscript main Abstract/Results pages1–4 and Figures1/2/4; supplementary Methods and raw data not reanalysed.. Claim fit: NLS-reporter rupture, defined in-vitro and mouse-dermis models, deformation-associated damage foci and ESCRT-III-dependent resealing independently match primary main Results/Figures. Mixed-topic Scite opening excluded.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies.
Sources and access depth (17)
Simple rules for passive diffusion through the nuclear pore complex — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus — primary. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Ran-system asymmetry regulates particular import/export reporters; not all cargo uses the same energy mechanism.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Mapping eGFP Oligomer Mobility in Living Cell Nuclei — primary. Access: Primary PLOS main Abstract, Methods data analysis/acquisition/calibration and selected Results/Discussion; no raw data reanalysis.. Claim fit: eGFP oligomer FCS outside nucleoli: calibrated two-normal-diffusion components plus triplet term; cell/model/probe constraints retained.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Reaction-diffusion FRAP solutions constrain binding inference; not every recovery curve identifies every parameter.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Coexisting Liquid Phases Underlie Nucleolar Subcompartments — primary. Access: Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.. Claim fit: Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Mapping and engineering RNA-driven architecture of the multiphase nucleolus — primary. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Quinodoz and colleagues spatially mapped rRNA maturation and engineered nucleoli with processing defects. Disrupting small-subunit processing reordered nucleolar layers and blocked normal rRNA outflux. This provides a substrate-linked perturbation of multiphase architecture, complementary to earlier material measurements. It does not establish that every nuclear body contains a permanent solid core or that all RNA-protein assemblies use the same phase mechanism. Quinodoz et al. (2025) .. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Karyopherins remodel the dynamic organization of the nuclear pore complex transport barrier — primary. Access: Publisher primary Abstract, opening Results on isolated yeast NPCs, selected DNA-origami Results and Discussion read; entire Methods and supplements not appraised.. Claim fit: High-speed AFM of isolated yeast NPCs and orthogonal approaches; transport-factor-dependent FG organization, mobile central cluster, altered FG mutants, and contrast with hydrogels.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Nuclear pore permeability and fluid flow are modulated by its dilation state — primary. Access: Consensus fetched primary record and search-returned primary abstract; full Results inaccessible. Online 2024; issue year should not replace online publication date.. Claim fit: Dictyostelium osmotic adaptation, dilation-dependent pressure-driven nucleocytosolic fluid flow and viral blockage; not identical to diffusion or receptor-driven transport.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes — primary. Access: Fetched primary abstract and publisher Results excerpts on Xenopus assembly and density model; Crossmark publication date and author metadata checked. Complete body and supplements not appraised.. Claim fit: Nuclear/cytoplasmic density differences and pressure-balance model constrained by transport, chromatin and embryo observations. Erroneous2023 provider year corrected to publisher15August2025.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Characterisation of the passive permeability barrier of nuclear pore complexes — primary. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Probe passage in permeabilized nuclei and barrier perturbations; distinct from living-yeast passive exchange.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility — primary. Access: Published identity and primary abstract from author-manuscript repository; full main text not appraised.. Claim fit: Differently sized inert GFP probes and polymer simulations; size-dependent intermediate-scale viscoelastic behavior and obstacle-network model; not universal fixed fractal organization.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Robust model-based analysis of single-particle tracking experiments with Spot-On — primary. Access: Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.. Claim fit: Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.. Limits: No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota.
Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores — primary. Access: Publisher primary selected Results on force application and import/export plus AFM Methods excerpt read; complete body and supplements not appraised.. Claim fit: Force-dependent YAP entry in defined fibroblast/MCF10A systems, nuclear deformation and import-rate assays; not all cargo or universal pore-mechanics explanation.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force — primary. Access: Primary manuscript main Summary, Results on microrheology and mechanomemory, Figures 1–5 and Discussion read; supplemental figures and raw measurements not reanalysed.. Claim fit: 200-nm-diameter targeted magnetic particles in CHO DHFR reporter nuclei; 0.1–5 Hz force response and separate hiPSC Pol II arm; local perturbation and injection limitations.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
Visualizing nuclear pore complex plasticity with pan-expansion microscopy — primary. Access: Fetched primary abstract and publication record; full Methods and Results not yet appraised.. Claim fit: Expanded fixed-cell NPC diameter distributions, nuclear-surface bias, hyperosmotic constriction and LINC perturbation; one patient-derived neuronal comparison does not establish all ALS.. Limits: No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.
This scholarly synthesis integrates foundational studies and literature available by 12 October 2026. Source access ranges from primary abstracts to selected Results, figure captions and Methods, as specified for each reference. Experiments and models retain their organism, construct and perturbation context; raw data and supplementary material have not been comprehensively reanalysed.
Sources and access depth (15)
The C-terminal domain of RNA polymerase II couples mRNA processing to transcription — primary. Access: Primary publication abstract and bibliographic record. Claim fit: CTD truncation inhibits efficient splicing, 3′ processing and termination in tested cellular context.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Nuclear export is a limiting factor in eukaryotic mRNA metabolism — primary. Access: SciSpace original publication abstract and journal/author/DOI metadata. Claim fit: Compartmental SLAM-seq and model estimate synthesis, export and degradation in human cancer cells.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Genome organization around nuclear speckles drives mRNA splicing efficiency — primary. Access: Consensus fetched primary abstract; publisher abstract and figure-caption descriptions. Claim fit: Speckle-proximal spliceosome binding and splicing; directed RNA recruitment tests spatial sufficiency.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Nuclear speckles enable processing of RNA from GC-rich isochores — primary. Access: Consensus fetched identity; SciSpace and PubMed primary abstract; actual PMC13283296 selected main Results/Fig1–4 captions. Claim fit: Acute SON/SRRM2 loss in human cells affects short GC-rich intron processing and accumulated RNA more than nascent RNA; protein loss and architecture remain coupled. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
An ATP-gated molecular switch orchestrates human mRNA export — primary. Access: Publisher primary model/Results discussion, Fig5 description and selected Methods. Claim fit: Structural/biochemical framework for UAP56 mRNP handoffs through TREX and TREX-2; online 2025, issue 2026.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1 — primary. Access: Scite primary main body introduction and targeted Results/figure excerpts. Claim fit: Three-hour architectural depletion in mESCs; most enhancer/promoter contact and transcription maintained, sensitive subsets and weak broad changes remain. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Coupling mRNA processing with transcription in time and space — seminal review. Access: Primary publication abstract and bibliographic record. Claim fit: Foundational mechanistic framework for co-transcriptional capping, splicing and 3′ processing.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution — primary. Access: Primary publication abstract and bibliographic record. Claim fit: Catalytic architecture of a crystallized ten-subunit yeast Pol II core; not a complete human initiation complex.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
In vivo dynamics of RNA polymerase II transcription — primary. Access: Primary manuscript introductory and model/results excerpts. Claim fit: Reporter fluorescence dynamics and deterministic model separate effective transcription stages.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Gene expression amplification by nuclear speckle association — primary. Access: Scite primary abstract; PubMed identity and selected primary figure context. Claim fit: Heat-shock Hsp70/HSPA1B RNA accumulation/proximity in human and hamster systems, reduced degradation contribution; not a pure initiation or splicing-rate measure. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Mammalian genes are transcribed with widely different bursting kinetics — primary. Access: Primary publication abstract and bibliographic record. Claim fit: Single-cell short-lived luciferase measurements and modeled gene-specific bursting; not direct nascent-RNA imaging.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
RBBP6 anchors pre-mRNA 3′ end processing to nuclear speckles for efficient gene expression — primary. Access: Root browser independently read actual PMC main Results, Fig1–6 captions, limitations and selected Methods; supplements and raw data not appraised. Claim fit: Domain-rescue experiments distinguish catalytic NTD from IDR4-supported spatial recruitment; APA/readthrough and RNA-localization outcomes retain model/assay context.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon–exon junctions — primary. Access: Primary manuscript abstract and selected Results/RNase-protection excerpts. Claim fit: Splicing-dependent deposited proteins in HeLa extract and Xenopus oocyte nuclei; export/decay roles discussed rather than all experimentally established.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
This scholarly synthesis integrates foundational studies and literature available by 12 October 2026. Source access ranges from primary abstracts to selected Results, figure captions and Methods, as specified for each reference. Experiments and models retain their organism, construct and perturbation context; raw data and supplementary material have not been comprehensively reanalysed.
Sources and access depth (9)
Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins — primary. Access: Scite identity; SciSpace primary abstract; root actual PMC3998805 main Results and Fig2/Fig3 captions. Claim fit: Oxidative PML mesh, subsequent SUMO/SIM partner retention, partner SUMOylation and selected RNF4 degradation; narrow CHO shell/core immuno-EM in Fig3B retained. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Cryo-EM structure of PML RBCC dimer reveals CC-mediated octopus-like nuclear body assembly mechanism — primary. Access: Publisher primary abstract, structural Results excerpts and bibliographic identity. Claim fit: RBCC dimer structural assembly model with coiled-coil interactions; no therapy/cure claim or whole-body phase diagnosis. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Dynamics of component exchange at PML nuclear bodies — primary. Access: Scite primary abstract + DOI metadata. Claim fit: Distinct PML isoform and partner exchange/retention; not a whole-body liquid phase measurement. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Induced proximity to PML protects TDP-43 from aggregation via SUMO–ubiquitin networks — primary. Access: Publisher primary abstract and Results opening; original PubMed metadata. Claim fit: SUMO2 fusion and engineered PML proximity reduce stress-induced insolubility; p97-dependent pathway.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Nuclear body phase separation drives telomere clustering in ALT cancer cells — primary. Access: Official PubMed primary abstract and metadata. Claim fit: Synthetic telomeric condensates test clustering versus ALT synthesis requirements.. Limits: Study-specific findings; no raw-data reanalysis or independent reproduction of experiments.
Scientific text and references appraised at recorded source depth · research
A recent measurement reinforces the need to match scale
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (4)
A three-dimensional model of the yeast genome — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Population genome contacts and constrained yeast reconstruction; no direct movie or universal species hierarchy.
Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy — primary study. Access: Bibliographic metadata and primary abstract via SciSpace/discovery where available; full-text retrieval failed after Scite quota.. Claim fit: Rahman and colleagues used multiplexed super-resolution fluorescence microscopy to compare thirteen nuclear targets. Associations evident at the micrometre scale could weaken or reverse at shorter scales. This provides an additional within-cell warning for species comparisons: matching an apparent compartment name does not guarantee that different assays resolve the same molecular organization. Rahman et al. (2025) .
Scientific text and references appraised at recorded source depth · research
TIMELESS has separable recruitment and turnover functions
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (4)
Poly(ADP-ribosyl)ation of TIMELESS limits DNA replication stress and promotes stalled fork protection — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Rageul and colleagues separately found that PARylation-dependent TIMELESS turnover supported stalled-fork protection. Retaining excess TIMELESS under their perturbations was detrimental, showing why recruitment during ongoing synthesis and regulated removal at stressed forks should not be summarized as a universal benefit of more TIMELESS. Rageul et al. (2024) .
The TIMELESS and PARP1 interaction suppresses replication-associated DNA gap accumulation — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: Saldanha and colleagues linked the TIMELESS–PARP1 interaction to backup Okazaki-fragment processing, XRCC1 recruitment and fewer post-replicative DNA gaps. Acute loss of TIMELESS and disruption of that interaction produced related defects in the tested cell systems. This extends the earlier checkpoint and cohesion evidence while keeping gaps, stalled forks and chromosome breaks as distinct readouts. Saldanha et al. (2024) .
This narrative integrates foundational and recent primary studies available by 12 October 2026. Source access ranges from original abstracts to selected Results, figure captions and Methods, as specified for each reference. It is a scholarly synthesis of the measured systems; it does not independently reproduce their experiments, analyze their raw data or establish exhaustive literature coverage.
Sources and access depth (12)
1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells — primary. Access: Prior audit selected original body passages; ledger re-read.. Claim fit: Histone-marker chromatin motion and compaction responses to hexanediol in human cell models.. Limits: Drug sensitivity is not a selective perturbation of phase separation.
Biomolecular condensates: organizers of cellular biochemistry — seminal review. Access: Consensus fetched review abstract; publisher body unavailable through web reader.. Claim fit: Definitions of membraneless concentration, multivalency and phase separation as an organizing framework.. Limits: Foundational framework; specific chromatin mechanisms are supported by primary experiments separately.
Mediator and RNA polymerase II clusters associate in transcription-dependent condensates — primary. Access: Consensus fetched original abstract in this rewrite; prior audit original captions and targeted excerpts.. Claim fit: Live mESC Mediator/Pol-II clusters, colocalization, exchange and transcription-inhibitor dependence.. Limits: Cluster properties support an assembly interpretation but do not uniquely isolate phase separation.
Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains — primary. Access: Prior audit original main Results and Figures 1–4; ledger and narrative re-read.. Claim fit: OCT4/MED1 selected mESC loci, purified MED1-IDR partitioning, acidic-residue mutant and reporter comparisons.. Limits: Activation-domain mutations can change ordinary coactivator contacts; not a fully phase-selective intervention.
Coactivator condensation at super-enhancers links phase separation and gene control — primary. Access: Consensus search and fetched original abstract inspected.. Claim fit: BRD4/MED1 cellular puncta and purified IDR droplet/nuclear-extract partitioning support a coactivator concentration model.. Limits: Abstract-bounded; solvent sensitivity does not alone establish a selective physical mechanism.
Imaging dynamic and selective low-complexity domain interactions that control gene transcription — primary. Access: SciSpace indexed original abstract and PubMed original metadata inspected.. Claim fit: Selective dynamic LCD hubs at synthetic/endogenous loci, Pol-II recruitment and activation without detectable phase separation under tested physiological conditions.. Limits: Study-specific hub regime; not proof against every condensate mechanism.
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation — primary. Access: SciSpace indexed original abstract inspected; prior audit source evidence reused.. Claim fit: Herpesviral replication-compartment Pol-II enrichment through accessible DNA interactions and repeated local visits.. Limits: Viral replication compartment is a mechanistic counterexample, not a replacement model for all host transcription.
Pol II phosphorylation regulates a switch between transcriptional and splicing condensates — primary. Access: Consensus fetched original abstract inspected.. Claim fit: CTD phosphorylation-dependent partition between Mediator and splicing-factor condensates.. Limits: Biochemical/selected cellular framework; complete path of each polymerase in an intact nucleus not traced.
Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription — primary. Access: Consensus fetched original abstract and publisher main Results/Figure 1 on phosphorylation/dephosphorylation and reaction controls inspected.. Claim fit: Reversible CTD phase behavior, partner-dependent phospho-CTD assemblies and cellular CTD-variant promoter/splicing comparisons.. Limits: Purified GST-CTD/crowding conditions and pleiotropic CTD variants; functional differences are not automatically phase-exclusive.
RNA-Mediated Feedback Control of Transcriptional Condensates — primary. Access: Original MIT author-repository abstract and publication identity inspected; Consensus fetched record contained takeaway only.. Claim fit: Nascent-RNA stimulation and later RNA-associated dissolution support a concentration-dependent transcriptional feedback model.. Limits: Original abstract-bounded qualitative finding; no quantitative RNA threshold or universal bursting rule claimed.
Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin — primary. Access: SciSpace original abstract and publisher original Results, Figures 1 and 7, K161A functional comparisons and Discussion inspected.. Claim fit: NDF–FACT heterotypic assembly, single-molecule chromatin elongation, retained-interaction/catalysis K161A comparison and human stem-cell FACT/elongation/nucleosome outcomes.. Limits: Selected main Results and captions; complete supplements and raw single-molecule data not reanalyzed; inference is specific to the tested elongation mechanism.
A single cluster of RNA Polymerase II molecules is stably associated with active genes — primary. Access: Consensus fetched original abstract; publisher 20 March 2026 date and selected original Results/Figures 1–2 inspected, plus prior audit main Results/Discussion.. Claim fit: Fly zygotic-genome-activation Pol-II clusters, initiation dependence, active-gene association and engaged-polymerase accumulation model.. Limits: Ordinary gene-associated embryonic clusters; histone-locus-body assemblies and other species/states remain separate. Consensus 2025 metadata overridden by verified publisher 2026 date.
Scientific text and references appraised at recorded source depth · research
A second virus example concerns a different physical question
Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth.
Sources and access depth (5)
Structure and gating of the nuclear pore complex — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: Xenopus oocyte NPC cryo-tomographic scaffold/channel structure; not direct universal transport kinetics.
The HIV capsid mimics karyopherin engagement of FG-nucleoporins — primary study. Access: Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.. Claim fit: The Dickson et al. (2024) showed FG-motif engagement by a capsid pocket and penetration of reconstituted FG nucleoporin condensates. Its karyopherin-mimicry interpretation concerns passage through a nuclear-barrier model. That is distinct from the Pol-II enrichment inside HSV1 replication compartments discussed above; evidence from either system should not be generalized to every viral nuclear route. Dickson et al. (2024) .
Simple rules for passive diffusion through the nuclear pore complex — primary study. Access: Primary abstract and bibliographic metadata; complete body unavailable through connector.. Claim fit: Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.
Robust model-based analysis of single-particle tracking experiments with Spot-On — primary study. Access: Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.. Claim fit: Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation — primary study. Access: Selected indexed primary main text (opening8000chars; not complete article), plus metadata.. Claim fit: HSV1-associated PolII enrichment consistent with accessible-DNA interactions in defined cells; not universal compartment mechanism.
Remaining limits
No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.
New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks.
Element maps had been equated directly with DNA/protein maps.
Archive motion, confinement and FRAP interpretation exceeded the measured observables.
The claim that most chromatin forms higher-order structures lacked a source and did not distinguish a regular fiber from heterogeneous organization.
Sources and access depth (7)
10.1046/j.1365-2818.1996.123403.x — primary study. Access: primary abstract via SciSpace; Scite metadata. Claim fit: elemental contrast and biochemical heterogeneity
10.1016/0889-1605(88)90032-8 — primary study. Access: Consensus fetch and Scite metadata; primary abstract available in search record. Claim fit: elemental phosphorus contrast in defined DNA specimens
10.1083/jcb.200507101 — primary study. Access: primary publication identity and abstract; selected PMC Results/figure excerpt from web search. Claim fit: GFP-actin R62D/latrunculin FRAP; no archive-specific validation
Atlas publisher correction was missing from source notes.
Method-paper identity does not authenticate each local crop; existing molecular-identity and display-motion caveats retained.
Sources and access depth (3)
10.1038/s41586-021-03992-4 — primary study. Access: Scite metadata plus primary PubMed abstract and selected figure descriptions read, PMID34616045; full Methods not appraised.. Claim fit: Ten whole-cell/tissue atlas datasets, FIB-SEM 4nm isotropic voxels and OpenOrganelle resource; individual local assets not authenticated.
10.1038/s41586-021-03977-3 — primary study. Access: Scite metadata plus primary PubMed abstract read, PMID34616042; full Methods not appraised.. Claim fit: Original organelle annotations, deep-learning segmentation in4nm/8nm volumes, correlative registration; no authentication of every local crop.
10.1038/s41586-021-04132-8 — editorial notice. Access: publisher correction notice full body at Nature lines 53-56. Claim fit: damaged supplementary video and axis-label formatting; no crop verification
Remaining limits
Individual image/dataset provenance, annotations and permissions unresolved.
Original detailed Results/Methods not freshly read through the APIs.