{ "edition_date": "2026-10-12", "topic_count": 23, "current_word_editions": 23, "preserved_original_word_files": 20, "scientific_words": 47351, "reference_entries": 375, "distinct_primary_studies": 168, "distinct_seminal_reviews": 7, "distinct_editorial_notices": 3, "scope": "Complete new narratives for the 23 canonical topics linked from Downloads, in matching HTML and Word editions. 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sufficiency in the defined preparation.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "ganji2018", "doi": "10.1126/science.aar7831", "title": "Real-time imaging of DNA loop extrusion by condensin", "authors": "Ganji M, Shaltiel IA, Bisht S, et al.", "year": 2018, "journal": "Science 360:102–105", "source_type": "primary", "url": "https://doi.org/10.1126/science.aar7831", "access_depth": "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.", "limitations": "Purified DNA assay; cellular loop paths and complete chromosome assembly not directly observed." }, { "id": "gibcus2018", "doi": "10.1126/science.aao6135", "title": "A pathway for mitotic chromosome formation", "authors": "Gibcus JH, Samejima K, Goloborodko A, et al.", "year": 2018, "journal": "Science 359:eaao6135", "source_type": "primary", "url": "https://doi.org/10.1126/science.aao6135", "access_depth": "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.", "limitations": "Population contacts and polymer-model fit; supplements and raw contact data not reanalyzed." }, { "id": "walther2018", "doi": "10.1083/jcb.201801048", "title": "A quantitative map of human Condensins provides new insights into mitotic chromosome architecture", "authors": "Walther N, Hossain MJ, Politi AZ, et al.", "year": 2018, "journal": "Journal of Cell Biology 217:2309–2328", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201801048", "access_depth": "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.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "nishino2012", "doi": "10.1038/emboj.2012.35", "title": "Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure", "authors": "Nishino Y, Eltsov M, Joti Y, et al.", "year": 2012, "journal": "EMBO Journal 31:1644–1653", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2012.35", "access_depth": "Prior focused audit original Results, captions, Discussion and main Methods; later DOI recheck abstract.", "claim_fit": "Isolated HeLa mitotic chromosome packing and ribosome-associated scattering; ordered chicken-erythrocyte control.", "limitations": "Isolation, washing and cryosectioning; not complete exclusion of local or specialized ordered fibers." }, { "id": "samejima2025", "doi": "10.1126/science.adq1709", "title": "Rules of engagement for condensins and cohesins guide mitotic chromosome formation", "authors": "Samejima K, Gibcus JH, Abraham S, et al.", "year": 2025, "journal": "Science 388:eadq1709", "source_type": "primary", "url": "https://doi.org/10.1126/science.adq1709", "access_depth": "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.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "tsubota2025", "doi": "10.1038/s41467-025-62600-5", "title": "Functional interplay between condensin I and topoisomerase IIα in single-molecule DNA compaction", "authors": "Tsubota Y, Shintomi K, Kinoshita K, et al.", "year": 2025, "journal": "Nature Communications 16", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-62600-5", "access_depth": "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.", "limitations": "Naked-DNA single-molecule system; cellular topological resolution cannot be inferred from knots in a reconstitution." }, { "id": "ono2004", "doi": "10.1242/jcs.01604", "title": "Distinct functions of condensin I and II in mitotic chromosome assembly", "authors": "Hirota T, Gerlich D, Koch B, Ellenberg J, Peters JM", "year": 2004, "journal": "Journal of Cell Science 117:6435–6445", "source_type": "primary", "url": "https://doi.org/10.1242/jcs.01604", "access_depth": "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.", "limitations": "Source abstract; detailed cell-line and depletion-efficiency claims omitted." }, { "id": "capture2023", "doi": "10.1016/j.molcel.2023.09.019", "title": "Establishment of dsDNA-dsDNA interactions by the condensin complex", "authors": "Tang M, Pobegalov G, Tanizawa H, et al.", "year": 2023, "journal": "Molecular Cell 83:3787–3800.e9", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2023.09.019", "access_depth": "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.", "limitations": "Abstract-bounded interpretation; not evidence that all cellular chromosome construction uses capture instead of extrusion." }, { "id": "chan2004", "doi": "10.1083/jcb.200408061", "title": "Condensin restructures chromosomes in preparation for meiotic divisions", "authors": "Chan RC, Severson AF, Meyer BJ", "year": 2004, "journal": "Journal of Cell Biology 167:613–625", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.200408061", "access_depth": "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.", "limitations": "Original abstract-bounded; not a claim that all meiotic species share vertebrate mitotic architecture." } ], "original_drafts": [ { "path": "Reviews_useredit/Chromosome Condensation_ Mechanisms and Choreograp.._.docx", "sha256": "4d6046e4e39860aaca638f2cfbfb753fb6194e96df6713e95dd65258427be5f6" } ] }, { "slug": "chromatin-biophysics", "title": "Chromatin biophysics: nucleosome interactions, genome folding and mechanical response", "subtitle": "A multiscale account connecting molecular accessibility to heterogeneous structure, chromosome dynamics and force transmission.", "group": "chromatin", "html_path": "nuclear_biology_reviews/reviews/chromatin_biophysics_comprehensive_review.html", "word_path": "Reviews_useredit/current_2026-10-12/chromatin-biophysics.docx", "scientific_words": 2100, "scientific_blocks": 34, "reference_count": 22, "sections": 10, "pages": 9, "html_sha256": "34b26007fb6725fc933c51fbdcb02e601f51aebfcee29cd1f46ccd3d450ae209", "word_sha256": "c88071bb78a65cce0b6ab304c12e8d6d5e649c1e494371d2839afd89eb423c1e", "content_sha256": "df69dce043b6dc35aecb78d6005d70a65da8f0119b041cb3b3e1304a221c4030", "parity": { "scientific_blocks_matched": 34, "reference_hyperlinks_matched": 22 }, "source_scope": "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.", "references": [ { "id": "shintomi2015", "doi": "10.1038/ncb3187", "title": "Reconstitution of mitotic chromatids with a minimum set of purified factors", "authors": "Shintomi K, Takahashi TS, Hirano T", "year": 2015, "journal": "Nature Cell Biology 17:1014–1023", "source_type": "primary", "url": "https://doi.org/10.1038/ncb3187", "access_depth": "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.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "ganji2018", "doi": "10.1126/science.aar7831", "title": "Real-time imaging of DNA loop extrusion by condensin", "authors": "Ganji M, Shaltiel IA, Bisht S, et al.", "year": 2018, "journal": "Science 360:102–105", "source_type": "primary", "url": "https://doi.org/10.1126/science.aar7831", "access_depth": "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.", "limitations": "Purified DNA assay; cellular loop paths and complete chromosome assembly not directly observed." }, { "id": "gibcus2018", "doi": "10.1126/science.aao6135", "title": "A pathway for mitotic chromosome formation", "authors": "Gibcus JH, Samejima K, Goloborodko A, et al.", "year": 2018, "journal": "Science 359:eaao6135", "source_type": "primary", "url": "https://doi.org/10.1126/science.aao6135", "access_depth": "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.", "limitations": "Population contacts and polymer-model fit; supplements and raw contact data not reanalyzed." }, { "id": "walther2018", "doi": "10.1083/jcb.201801048", "title": "A quantitative map of human Condensins provides new insights into mitotic chromosome architecture", "authors": "Walther N, Hossain MJ, Politi AZ, et al.", "year": 2018, "journal": "Journal of Cell Biology 217:2309–2328", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201801048", "access_depth": "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.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "nishino2012", "doi": "10.1038/emboj.2012.35", "title": "Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure", "authors": "Nishino Y, Eltsov M, Joti Y, et al.", "year": 2012, "journal": "EMBO Journal 31:1644–1653", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2012.35", "access_depth": "Prior focused audit original Results, captions, Discussion and main Methods; later DOI recheck abstract.", "claim_fit": "Isolated HeLa mitotic chromosome packing and ribosome-associated scattering; ordered chicken-erythrocyte control.", "limitations": "Isolation, washing and cryosectioning; not complete exclusion of local or specialized ordered fibers." }, { "id": "samejima2025", "doi": "10.1126/science.adq1709", "title": "Rules of engagement for condensins and cohesins guide mitotic chromosome formation", "authors": "Samejima K, Gibcus JH, Abraham S, et al.", "year": 2025, "journal": "Science 388:eadq1709", "source_type": "primary", "url": "https://doi.org/10.1126/science.adq1709", "access_depth": "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.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "luger1997", "doi": "10.1038/38444", "title": "Crystal structure of the nucleosome core particle at 2.8 Å resolution", "authors": "Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ", "year": 1997, "journal": "Nature 389:251–260", "source_type": "primary", "url": "https://doi.org/10.1038/38444", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Histone octamer, DNA superhelix and histone-tail contacts in the crystallized nucleosome.", "limitations": "Crystallized core particle; not a direct measurement of chromatin dynamics or whole-nucleus packing." }, { "id": "polach1995", "doi": "10.1006/jmbi.1995.0606", "title": "Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation", "authors": "Polach KJ, Widom J", "year": 1995, "journal": "Journal of Molecular Biology 254:130–149", "source_type": "primary", "url": "https://doi.org/10.1006/jmbi.1995.0606", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Restriction-accessibility kinetics support transient site exposure and a position-dependent equilibrium model.", "limitations": "Reconstituted substrate and model inference; not a direct in-vivo accessibility rate." }, { "id": "cui2000", "doi": "10.1073/pnas.97.1.127", "title": "Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure", "authors": "Cui Y, Bustamante C", "year": 2000, "journal": "PNAS 97:127–132", "source_type": "primary", "url": "https://doi.org/10.1073/pnas.97.1.127", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Chicken erythrocyte fiber stretch/release, ionic-strength dependence and irreversible high-force changes.", "limitations": "Isolated specialized chromatin; fitted persistence length and force transitions not universal nuclear constants." }, { "id": "routh2008", "doi": "10.1073/pnas.0802336105", "title": "Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure", "authors": "Routh A, Sandin S, Rhodes D", "year": 2008, "journal": "PNAS 105:8872–8877", "source_type": "primary", "url": "https://doi.org/10.1073/pnas.0802336105", "access_depth": "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.", "limitations": "Artificial arrays and negative-stain EM; no direct living-cell fiber census." }, { "id": "h4k16", "doi": "10.1126/science.1124000", "title": "Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions", "authors": "Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL", "year": 2006, "journal": "Science 311:844–847", "source_type": "primary", "url": "https://doi.org/10.1126/science.1124000", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Chemically defined H4K16-acetylated arrays inhibit folding and cross-fiber interactions and alter ACF remodeling.", "limitations": "Defined in-vitro substrate; not evidence that all acetylation effects in cells are direct fiber unfolding." }, { "id": "gibson2019", "doi": "10.1016/j.cell.2019.08.037", "title": "Organization of Chromatin by Intrinsic and Regulated Phase Separation", "authors": "Gibson BA, Doolittle LK, Schneider MWG, et al.", "year": 2019, "journal": "Cell 179:470–484.e21", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2019.08.037", "access_depth": "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.", "limitations": "Purified arrays under stated conditions; a cellular phase mechanism is not inferred for all chromatin." }, { "id": "erdel2020", "doi": "10.1016/j.molcel.2020.02.005", "title": "Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation", "authors": "Erdel F, Rademacher A, Vlijm R, et al.", "year": 2020, "journal": "Molecular Cell 78:236–249.e7", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2020.02.005", "access_depth": "Prior audit selected original main Results and indexed body; ledger re-read.", "claim_fit": "Mouse fibroblast chromocenter compaction and HP1 partition/perturbation measurements; absence of tested HP1-liquid hallmarks.", "limitations": "Specific pericentric foci, not every heterochromatin domain or every chromatin-condensation mechanism." }, { "id": "hou2023", "doi": "10.1038/s41467-023-42072-1", "title": "Structure of native chromatin fibres revealed by Cryo-ET in situ", "authors": "Hou Z, Nightingale F, Zhu Y, MacGregor-Chatwin C, Zhang P", "year": 2023, "journal": "Nature Communications 14:6324", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-023-42072-1", "access_depth": "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.", "limitations": "Limited cryogenic volumes and cellular model; local arrangements do not define a genome-wide polymer conformation." }, { "id": "kreysing2026", "doi": "10.1038/s41467-026-75087-5", "title": "Molecular architecture of heterochromatin at the nuclear periphery of primary human cells", "authors": "Kreysing JP, Cruz-León S, Betz J, et al.", "year": 2026, "journal": "Nature Communications 17:5844", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-026-75087-5", "access_depth": "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.", "limitations": "Selected cellular region and quiescent state; observed envelope width is not proof of canonical fiber periodicity." }, { "id": "xie2026", "doi": "10.1093/nsr/nwaf451", "title": "MINFLUX dissects nucleosome and compacting chromatin structures in living cells", "authors": "Xie H, Hu Y, Cheng R, et al.", "year": 2026, "journal": "National Science Review 13:nwaf451; online 21 October 2025", "source_type": "primary", "url": "https://doi.org/10.1093/nsr/nwaf451", "access_depth": "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.", "limitations": "AT-preferring probe, selected trajectories and possible probe stabilization; localization precision differs from structural resolution." }, { "id": "gabriele2022", "doi": "10.1126/science.abn6583", "title": "Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging", "authors": "Gabriele M, Brandão HB, Grosse-Holz S, et al.", "year": 2022, "journal": "Science 376:496–501", "source_type": "primary", "url": "https://doi.org/10.1126/science.abn6583", "access_depth": "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.", "limitations": "One silent 505-kb locus in mESC G1/early S; model-inferred state and lifetime, not direct extrusion movies." }, { "id": "brackley2013", "doi": "10.1073/pnas.1302950110", "title": "Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization", "authors": "Brackley CA, Taylor S, Papantonis A, Cook PR, Marenduzzo D", "year": 2013, "journal": "PNAS 110:E3605–E3611", "source_type": "primary", "url": "https://doi.org/10.1073/pnas.1302950110", "access_depth": "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.", "limitations": "Coarse-grained equilibrium model; not proof that a specific nuclear assembly is produced by bridging." }, { "id": "bensaha2025", "doi": "10.1038/s41467-025-61749-3", "title": "HP1 loses its chromatin clustering and phase separation function across evolution", "authors": "Bensaha S, Lewandowska D, Muzzopappa F, et al.", "year": 2025, "journal": "Nature Communications 16:6375", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-61749-3", "access_depth": "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.", "limitations": "GFP fusion/reconstitution and heterologous-expression contexts; not a census of all tissues or all HP1 functions." }, { "id": "stephens2017", "doi": "10.1091/mbc.E16-09-0653", "title": "Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus", "authors": "Stephens AD, Banigan EJ, Adam SA, Goldman RD, Marko JF", "year": 2017, "journal": "Molecular Biology of the Cell 28:1984–1996", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "access_depth": "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.", "limitations": "Isolated imposed-extension geometry; no universal chromatin modulus or nuclear viscosity." }, { "id": "bergamaschi2024", "doi": "10.1016/j.celrep.2024.114852", "title": "Heterogeneous force response of chromatin in isolated nuclei", "authors": "Bergamaschi G, Biebricher A, Witt H, et al.", "year": 2024, "journal": "Cell Reports 43:114852", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114852", "access_depth": "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.", "limitations": "Abstract-bounded; prepared nuclei and strain regime, not every live-cell mechanical context." }, { "id": "attar2025", "doi": "10.1093/nar/gkaf763", "title": "Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response", "authors": "Attar AG, Paturej J, Sarıyer OS, Banigan EJ, Erbaş A", "year": 2025, "journal": "Nucleic Acids Research 53:gkaf763", "source_type": "primary", "url": "https://doi.org/10.1093/nar/gkaf763", "access_depth": "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.", "limitations": "Model-supported account, not direct identification of every native molecular tether." } ], "original_drafts": [ { "path": "Reviews_useredit/Chromatin Biophysics and Function Review_.docx", "sha256": "a83c7e851ea165ef8559c036a17c8ff21771ff0e4c7fb54505177d091075c146" } ] }, { "slug": "chromatin-condensates", "title": "Chromatin condensates: mechanisms, evidence and cellular context", "subtitle": "What purified arrays and chromatin-binding proteins demonstrate, and how to distinguish phase separation from other forms of organization.", "group": "chromatin", "html_path": "nuclear_biology_reviews/reviews/chromatin-condensates-critical-review.html", "word_path": "Reviews_useredit/current_2026-10-12/chromatin-condensates.docx", "scientific_words": 2044, "scientific_blocks": 34, "reference_count": 14, "sections": 10, "pages": 8, "html_sha256": "829b11580e9d579c137669cccb41b89f5649dd963b53a25d06650e68028c9747", "word_sha256": "5d09d8c2957e71b277a1513dfe3aab04deb719013f09ca0650916c5e0ff9a923", "content_sha256": "841222c7e5b13f04649c9a84fecdd57dfd829c23edc6e8c7351ad4ce0315aee7", "parity": { "scientific_blocks_matched": 34, "reference_hyperlinks_matched": 14 }, "source_scope": "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. 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ledger re-read.", "claim_fit": "Mouse fibroblast chromocenter compaction and HP1 partition/perturbation measurements; absence of tested HP1-liquid hallmarks.", "limitations": "Specific pericentric foci, not every heterochromatin domain or every chromatin-condensation mechanism." }, { "id": "hou2023", "doi": "10.1038/s41467-023-42072-1", "title": "Structure of native chromatin fibres revealed by Cryo-ET in situ", "authors": "Hou Z, Nightingale F, Zhu Y, MacGregor-Chatwin C, Zhang P", "year": 2023, "journal": "Nature Communications 14:6324", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-023-42072-1", "access_depth": "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.", "limitations": "Limited cryogenic volumes and cellular model; local arrangements do not define a genome-wide polymer conformation." }, { "id": "kreysing2026", "doi": "10.1038/s41467-026-75087-5", "title": "Molecular architecture of heterochromatin at the nuclear periphery of primary human cells", "authors": "Kreysing JP, Cruz-León S, Betz J, et al.", "year": 2026, "journal": "Nature Communications 17:5844", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-026-75087-5", "access_depth": "Prior audit original publisher Results and Methods; 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ledger re-read.", "claim_fit": "Purified human HP1α, DNA, phosphorylation and partner partitioning demonstrate context-dependent droplet capacity.", "limitations": "In-vitro capacity is distinguished from a general mammalian cellular mechanism." }, { "id": "strom2017", "doi": "10.1038/nature22989", "title": "Phase separation drives heterochromatin domain formation", "authors": "Strom AR, Emelyanov AV, Mir M, et al.", "year": 2017, "journal": "Nature 547:241–245", "source_type": "primary", "url": "https://doi.org/10.1038/nature22989", "access_depth": "Prior audit original abstract; source narrative and ledger re-read.", "claim_fit": "Drosophila HP1a reconstitution and early embryonic liquid-like heterochromatin observations.", "limitations": "Early fly developmental context; detailed quantitative Methods not reappraised." }, { "id": "itoh2021", "doi": "10.26508/lsa.202001005", "title": "1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells", "authors": "Itoh Y, Iida S, Tamura S, et al.", "year": 2021, "journal": "Life Science Alliance 4:e202001005", "source_type": "primary", "url": "https://doi.org/10.26508/lsa.202001005", "access_depth": "Prior audit selected original body passages; ledger re-read.", "claim_fit": "Histone-marker chromatin motion and compaction responses to hexanediol in human cell models.", "limitations": "Drug sensitivity is not a selective perturbation of phase separation." }, { "id": "bensaha2025", "doi": "10.1038/s41467-025-61749-3", "title": "HP1 loses its chromatin clustering and phase separation function across evolution", "authors": "Bensaha S, Lewandowska D, Muzzopappa F, et al.", "year": 2025, "journal": "Nature Communications 16:6375", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-61749-3", "access_depth": "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.", "limitations": "GFP fusion/reconstitution and heterologous-expression contexts; not a census of all tissues or all HP1 functions." }, { "id": "banani2017", "doi": "10.1038/nrm.2017.7", "title": "Biomolecular condensates: organizers of cellular biochemistry", "authors": "Banani SF, Lee HO, Hyman AA, Rosen MK", "year": 2017, "journal": "Nature Reviews Molecular Cell Biology 18:285–298", "source_type": "seminal_review", "url": "https://doi.org/10.1038/nrm.2017.7", "access_depth": "Consensus fetched review abstract; publisher body unavailable through web reader.", "claim_fit": "Definitions of membraneless concentration, multivalency and phase separation as an organizing framework.", "limitations": "Foundational framework; specific chromatin mechanisms are supported by primary experiments separately.", "seminal_reason": "Widely used foundational synthesis that established the condensate organizing framework; retained for definitions, not as proof of a particular cellular phase mechanism." }, { "id": "lachner2001", "doi": "10.1038/35065132", "title": "Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins", "authors": "Lachner M, O’Carroll D, Rea S, Mechtler K, Jenuwein T", "year": 2001, "journal": "Nature 410:116–120", "source_type": "primary", "url": "https://doi.org/10.1038/35065132", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "HP1 chromodomain recognition of H3K9 methylation; Suv39h-double-null primary mouse fibroblast localization and catalytic rescue.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "bannister2001", "doi": "10.1038/35065138", "title": "Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain", "authors": "Bannister AJ, Zegerman P, Partridge JF, et al.", "year": 2001, "journal": "Nature 410:120–124", "source_type": "primary", "url": "https://doi.org/10.1038/35065138", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Specific methyl-lysine recognition and chromodomain-mutant comparisons; fission-yeast silencing context.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." } ], "original_drafts": [ { "path": "Reviews_useredit/Chromatin Condensates_ Existence and Function.docx", "sha256": "f00d6111c7e8d01b2158d235478b04279f5098cbbfc3b8c2a5398bf5433d9b8f" } ] }, { "slug": "euchromatin", "title": "Euchromatin: accessibility, regulatory competence and dynamic genome organization", "subtitle": "A current synthesis of how nucleosomes, remodeling, regulatory elements and chromosome folding support an accessible genome.", "group": "chromatin", "html_path": "nuclear_biology_reviews/reviews/euchromatin-comprehensive-review.html", "word_path": "Reviews_useredit/current_2026-10-12/euchromatin.docx", "scientific_words": 2041, "scientific_blocks": 34, "reference_count": 19, "sections": 10, "pages": 8, "html_sha256": "55f0a8f65b86d09ebadb4e61764058024b9054839df710b744bf388b33217517", "word_sha256": "a39f1a23f6a95ba460ba1a71307a876a009f194c194aa2eeca7abd14ebc958e8", "content_sha256": "0f95e14efe3e8485f6b1393768962f84d2ae2a4886ebb39e64cabd45e6c37bfc", "parity": { "scientific_blocks_matched": 34, "reference_hyperlinks_matched": 19 }, "source_scope": "This narrative integrates foundational and recent primary studies available by 12 October 2026. 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ledger re-read.", "claim_fit": "Resting primary human CD4+ T-cell peripheral chromatin, heterogeneous elongated arrangement and frequent nucleosome stacking.", "limitations": "Selected cellular region and quiescent state; observed envelope width is not proof of canonical fiber periodicity." }, { "id": "gabriele2022", "doi": "10.1126/science.abn6583", "title": "Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging", "authors": "Gabriele M, Brandão HB, Grosse-Holz S, et al.", "year": 2022, "journal": "Science 376:496–501", "source_type": "primary", "url": "https://doi.org/10.1126/science.abn6583", "access_depth": "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.", "limitations": "One silent 505-kb locus in mESC G1/early S; model-inferred state and lifetime, not direct extrusion movies." }, { "id": "zhang2024", "doi": "10.1038/s41556-024-01547-z", "title": "Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells", "authors": "Zhang J, Donahue G, Gilbert MB, Lapidot T, Nicetto D, Zaret KS", "year": 2024, "journal": "Nature Cell Biology 26:2115–2128", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-024-01547-z", "access_depth": "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.", "limitations": "Abstract-bounded; four stability classes in this engineered pluripotent-cell context, not universal decay constants." }, { "id": "atac2013", "doi": "10.1038/nmeth.2688", "title": "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position", "authors": "Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ", "year": 2013, "journal": "Nature Methods 10:1213–1218", "source_type": "primary", "url": "https://doi.org/10.1038/nmeth.2688", "access_depth": "Prior audit selected original main body; ledger re-read.", "claim_fit": "ATAC-seq Tn5 insertion and fragment-pattern readouts; accessibility assay distinguished from direct transcription or physical porosity.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "rao2014", "doi": "10.1016/j.cell.2014.11.021", "title": "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping", "authors": "Rao SSP, Huntley MH, Durand NC, et al.", "year": 2014, "journal": "Cell 159:1665–1680", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2014.11.021", "access_depth": "Prior audit original abstract plus selected indexed results; 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ledger re-read.", "claim_fit": "Selected chromosome-21 fixed-cell intervals; variable domain boundaries and cohesin-depleted HCT116 comparisons.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "ou2017", "doi": "10.1126/science.aag0025", "title": "ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells", "authors": "Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O’Shea CC", "year": 2017, "journal": "Science 357:eaag0025", "source_type": "primary", "url": "https://doi.org/10.1126/science.aag0025", "access_depth": "Prior audit selected original body and captions; ledger re-read.", "claim_fit": "Disordered chromatin chains and heterogeneous packing in sampled human cellular preparations.", "limitations": "Fixed and processed structural specimen; not a live dynamics assay." }, { "id": "heintzman2009", "doi": "10.1038/nature07829", "title": "Histone modifications at human enhancers reflect global cell-type-specific gene expression", "authors": "Heintzman ND, Hon GC, Hawkins RD, et al.", "year": 2009, "journal": "Nature 459:108–112", "source_type": "primary", "url": "https://doi.org/10.1038/nature07829", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Multi-cell-type chromatin maps and enhancer activity associate enhancer signatures with cell-specific expression programs.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "soufi2015", "doi": "10.1016/j.cell.2015.03.017", "title": "Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming", "authors": "Soufi A, Garcia MF, Jaroszewicz A, Osman N, Pellegrini M, Zaret KS", "year": 2015, "journal": "Cell 161:555–568", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2015.03.017", "access_depth": "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.", "limitations": "Full Results not appraised; c-Myc must not be grouped with the three factors as an equally demonstrated nucleosome-binding pioneer." }, { "id": "basurto2024", "doi": "10.1016/j.celrep.2024.113855", "title": "SWI/SNF-dependent genes are defined by their chromatin landscape", "authors": "Basurto-Cayuela L, Guerrero-Martínez JA, Gómez-Marín E, et al.", "year": 2024, "journal": "Cell Reports 43:113855", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.113855", "access_depth": "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.", "limitations": "No complete original main Results or supplementary analysis inspected." }, { "id": "alabert2015", "doi": "10.1101/gad.256354.114", "title": "Two distinct modes for propagation of histone PTMs across the cell cycle", "authors": "Alabert C, Barth TK, Reverón-Gómez N, et al.", "year": 2015, "journal": "Genes & Development 29:585–590", "source_type": "primary", "url": "https://doi.org/10.1101/gad.256354.114", "access_depth": "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.", "limitations": "Population peptides, not genomic address or every pair of modifications on one nucleosome; supplementary cell-line details not appraised." }, { "id": "liu2023", "doi": "10.1038/s41467-023-39846-y", "title": "Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction", "authors": "Liu C, Yu J, Song A, et al.", "year": 2023, "journal": "Nature Communications 14:4081", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-023-39846-y", "access_depth": "Prior audit original selected Results and Discussion; 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ledger re-read.", "claim_fit": "Mouse fibroblast chromocenter compaction and HP1 partition/perturbation measurements; absence of tested HP1-liquid hallmarks.", "limitations": "Specific pericentric foci, not every heterochromatin domain or every chromatin-condensation mechanism." }, { "id": "hou2023", "doi": "10.1038/s41467-023-42072-1", "title": "Structure of native chromatin fibres revealed by Cryo-ET in situ", "authors": "Hou Z, Nightingale F, Zhu Y, MacGregor-Chatwin C, Zhang P", "year": 2023, "journal": "Nature Communications 14:6324", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-023-42072-1", "access_depth": "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.", "limitations": "Limited cryogenic volumes and cellular model; local arrangements do not define a genome-wide polymer conformation." }, { "id": "kreysing2026", "doi": "10.1038/s41467-026-75087-5", "title": "Molecular architecture of heterochromatin at the nuclear periphery of primary human cells", "authors": "Kreysing JP, Cruz-León S, Betz J, et al.", "year": 2026, "journal": "Nature Communications 17:5844", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-026-75087-5", "access_depth": "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.", "limitations": "Selected cellular region and quiescent state; observed envelope width is not proof of canonical fiber periodicity." }, { "id": "xie2026", "doi": "10.1093/nsr/nwaf451", "title": "MINFLUX dissects nucleosome and compacting chromatin structures in living cells", "authors": "Xie H, Hu Y, Cheng R, et al.", "year": 2026, "journal": "National Science Review 13:nwaf451; online 21 October 2025", "source_type": "primary", "url": "https://doi.org/10.1093/nsr/nwaf451", "access_depth": "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.", "limitations": "AT-preferring probe, selected trajectories and possible probe stabilization; localization precision differs from structural resolution." }, { "id": "brackley2013", "doi": "10.1073/pnas.1302950110", "title": "Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization", "authors": "Brackley CA, Taylor S, Papantonis A, Cook PR, Marenduzzo D", "year": 2013, "journal": "PNAS 110:E3605–E3611", "source_type": "primary", "url": "https://doi.org/10.1073/pnas.1302950110", "access_depth": "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.", "limitations": "Coarse-grained equilibrium model; not proof that a specific nuclear assembly is produced by bridging." }, { "id": "larson2017", "doi": "10.1038/nature22822", "title": "Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin", "authors": "Larson AG, Elnatan D, Keenen MM, et al.", "year": 2017, "journal": "Nature 547:236–240", "source_type": "primary", "url": "https://doi.org/10.1038/nature22822", "access_depth": "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.", "limitations": "In-vitro capacity is distinguished from a general mammalian cellular mechanism." }, { "id": "strom2017", "doi": "10.1038/nature22989", "title": "Phase separation drives heterochromatin domain formation", "authors": "Strom AR, Emelyanov AV, Mir M, et al.", "year": 2017, "journal": "Nature 547:241–245", "source_type": "primary", "url": "https://doi.org/10.1038/nature22989", "access_depth": "Prior audit original abstract; source narrative and ledger re-read.", "claim_fit": "Drosophila HP1a reconstitution and early embryonic liquid-like heterochromatin observations.", "limitations": "Early fly developmental context; detailed quantitative Methods not reappraised." }, { "id": "bensaha2025", "doi": "10.1038/s41467-025-61749-3", "title": "HP1 loses its chromatin clustering and phase separation function across evolution", "authors": "Bensaha S, Lewandowska D, Muzzopappa F, et al.", "year": 2025, "journal": "Nature Communications 16:6375", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-61749-3", "access_depth": "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.", "limitations": "GFP fusion/reconstitution and heterologous-expression contexts; 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online 13 December 2017", "source_type": "seminal_review", "url": "https://doi.org/10.1038/nrm.2017.119", "access_depth": "Consensus fetched review abstract and original publisher Key Points inspected.", "claim_fit": "Foundational distinctions among nucleation, spreading, maintenance, repetitive-DNA functions and lineage restriction.", "limitations": "Conceptual definitions supported by the seminal review; particular contemporary mechanisms cited to primary work.", "seminal_reason": "Foundational cross-species synthesis of establishment, spreading and inheritance principles, used for terminology and the organizing framework." }, { "id": "zhang2024", "doi": "10.1038/s41556-024-01547-z", "title": "Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells", "authors": "Zhang J, Donahue G, Gilbert MB, Lapidot T, Nicetto D, Zaret KS", "year": 2024, "journal": "Nature Cell Biology 26:2115–2128", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-024-01547-z", "access_depth": "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.", "limitations": "Abstract-bounded; four stability classes in this engineered pluripotent-cell context, not universal decay constants." }, { "id": "alabert2015", "doi": "10.1101/gad.256354.114", "title": "Two distinct modes for propagation of histone PTMs across the cell cycle", "authors": "Alabert C, Barth TK, Reverón-Gómez N, et al.", "year": 2015, "journal": "Genes & Development 29:585–590", "source_type": "primary", "url": "https://doi.org/10.1101/gad.256354.114", "access_depth": "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.", "limitations": "Population peptides, not genomic address or every pair of modifications on one nucleosome; supplementary cell-line details not appraised." }, { "id": "liu2023", "doi": "10.1038/s41467-023-39846-y", "title": "Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction", "authors": "Liu C, Yu J, Song A, et al.", "year": 2023, "journal": "Nature Communications 14:4081", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-023-39846-y", "access_depth": "Prior audit original selected Results and Discussion; 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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.", "references": [ { "id": "luger1997", "doi": "10.1038/38444", "title": "Crystal structure of the nucleosome core particle at 2.8 Å resolution", "authors": "Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ", "year": 1997, "journal": "Nature 389:251–260", "source_type": "primary", "url": "https://doi.org/10.1038/38444", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Histone octamer, DNA superhelix and histone-tail contacts in the crystallized nucleosome.", "limitations": "Crystallized core particle; not a direct measurement of chromatin dynamics or whole-nucleus packing." }, { "id": "routh2008", "doi": "10.1073/pnas.0802336105", "title": "Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure", "authors": "Routh A, Sandin S, Rhodes D", "year": 2008, "journal": "PNAS 105:8872–8877", "source_type": "primary", "url": "https://doi.org/10.1073/pnas.0802336105", "access_depth": "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.", "limitations": "Artificial arrays and negative-stain EM; no direct living-cell fiber census." }, { "id": "h4k16", "doi": "10.1126/science.1124000", "title": "Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions", "authors": "Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL", "year": 2006, "journal": "Science 311:844–847", "source_type": "primary", "url": "https://doi.org/10.1126/science.1124000", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Chemically defined H4K16-acetylated arrays inhibit folding and cross-fiber interactions and alter ACF remodeling.", "limitations": "Defined in-vitro substrate; not evidence that all acetylation effects in cells are direct fiber unfolding." }, { "id": "gibson2019", "doi": "10.1016/j.cell.2019.08.037", "title": "Organization of Chromatin by Intrinsic and Regulated Phase Separation", "authors": "Gibson BA, Doolittle LK, Schneider MWG, et al.", "year": 2019, "journal": "Cell 179:470–484.e21", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2019.08.037", "access_depth": "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.", "limitations": "Purified arrays under stated conditions; a cellular phase mechanism is not inferred for all chromatin." }, { "id": "lachner2001", "doi": "10.1038/35065132", "title": "Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins", "authors": "Lachner M, O’Carroll D, Rea S, Mechtler K, Jenuwein T", "year": 2001, "journal": "Nature 410:116–120", "source_type": "primary", "url": "https://doi.org/10.1038/35065132", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "HP1 chromodomain recognition of H3K9 methylation; Suv39h-double-null primary mouse fibroblast localization and catalytic rescue.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "bannister2001", "doi": "10.1038/35065138", "title": "Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain", "authors": "Bannister AJ, Zegerman P, Partridge JF, et al.", "year": 2001, "journal": "Nature 410:120–124", "source_type": "primary", "url": "https://doi.org/10.1038/35065138", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Specific methyl-lysine recognition and chromodomain-mutant comparisons; fission-yeast silencing context.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "margueron2009", "doi": "10.1038/nature08398", "title": "Role of the polycomb protein Eed in the propagation of repressive histone marks", "authors": "Margueron R, Justin N, Ohno K, et al.", "year": 2009, "journal": "Nature 461:762–767", "source_type": "primary", "url": "https://doi.org/10.1038/nature08398", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "EED recognition of repressive trimethyl-lysine marks and allosteric PRC2 activation; biochemical and fly-mutant evidence.", "limitations": "Reader–writer propagation model; does not alone prove a complete cellular inheritance mechanism." }, { "id": "zhang2024", "doi": "10.1038/s41556-024-01547-z", "title": "Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells", "authors": "Zhang J, Donahue G, Gilbert MB, Lapidot T, Nicetto D, Zaret KS", "year": 2024, "journal": "Nature Cell Biology 26:2115–2128", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-024-01547-z", "access_depth": "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.", "limitations": "Abstract-bounded; four stability classes in this engineered pluripotent-cell context, not universal decay constants." }, { "id": "atac2013", "doi": "10.1038/nmeth.2688", "title": "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position", "authors": "Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ", "year": 2013, "journal": "Nature Methods 10:1213–1218", "source_type": "primary", "url": "https://doi.org/10.1038/nmeth.2688", "access_depth": "Prior audit selected original main body; ledger re-read.", "claim_fit": "ATAC-seq Tn5 insertion and fragment-pattern readouts; accessibility assay distinguished from direct transcription or physical porosity.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "heintzman2009", "doi": "10.1038/nature07829", "title": "Histone modifications at human enhancers reflect global cell-type-specific gene expression", "authors": "Heintzman ND, Hon GC, Hawkins RD, et al.", "year": 2009, "journal": "Nature 459:108–112", "source_type": "primary", "url": "https://doi.org/10.1038/nature07829", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Multi-cell-type chromatin maps and enhancer activity associate enhancer signatures with cell-specific expression programs.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "basurto2024", "doi": "10.1016/j.celrep.2024.113855", "title": "SWI/SNF-dependent genes are defined by their chromatin landscape", "authors": "Basurto-Cayuela L, Guerrero-Martínez JA, Gómez-Marín E, et al.", "year": 2024, "journal": "Cell Reports 43:113855", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.113855", "access_depth": "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.", "limitations": "No complete original main Results or supplementary analysis inspected." }, { "id": "alabert2015", "doi": "10.1101/gad.256354.114", "title": "Two distinct modes for propagation of histone PTMs across the cell cycle", "authors": "Alabert C, Barth TK, Reverón-Gómez N, et al.", "year": 2015, "journal": "Genes & Development 29:585–590", "source_type": "primary", "url": "https://doi.org/10.1101/gad.256354.114", "access_depth": "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.", "limitations": "Population peptides, not genomic address or every pair of modifications on one nucleosome; supplementary cell-line details not appraised." }, { "id": "liu2023", "doi": "10.1038/s41467-023-39846-y", "title": "Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction", "authors": "Liu C, Yu J, Song A, et al.", "year": 2023, "journal": "Nature Communications 14:4081", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-023-39846-y", "access_depth": "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.", "limitations": "Ensemble occupancy and fitted restoration rates; chronic depletion may have indirect effects." }, { "id": "charlton2024", "doi": "10.1016/j.cell.2024.07.017", "title": "The fork protection complex promotes parental histone recycling and epigenetic memory", "authors": "Charlton SJ, Flury V, Kanoh Y, et al.", "year": 2024, "journal": "Cell 187:5029–5047.e21", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2024.07.017", "access_depth": "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.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "kouzarides2007", "doi": "10.1016/j.cell.2007.02.005", "title": "Chromatin Modifications and Their Function", "authors": "Kouzarides T", "year": 2007, "journal": "Cell 128:693–705", "source_type": "seminal_review", "url": "https://doi.org/10.1016/j.cell.2007.02.005", "access_depth": "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.", "limitations": "Historical review used for foundational principles; current claims cite original studies.", "seminal_reason": "Foundational synthesis that defined major functional routes for histone modifications; retained for chemical terminology and the causal framework." }, { "id": "you2013", "doi": "10.1038/nsmb.2476", "title": "Nuclear receptor co-repressors are required for the histone-deacetylase activity of HDAC3 in vivo", "authors": "You SH, Lim HW, Sun Z, Broache M, Won KJ, Lazar MA", "year": 2013, "journal": "Nature Structural & Molecular Biology 20:182–187", "source_type": "primary", "url": "https://doi.org/10.1038/nsmb.2476", "access_depth": "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.", "limitations": "Recruitment also changes; activity below assay background cannot be excluded and all HDACs are not equivalent." }, { "id": "egelhofer2011", "doi": "10.1038/nsmb.1972", "title": "An assessment of histone-modification antibody quality", "authors": "Egelhofer TA, Minoda A, Klugman S, et al.", "year": 2011, "journal": "Nature Structural & Molecular Biology 18:91–93; 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ledger re-read.", "claim_fit": "NCoR/SMRT activation-domain mutant mice separate retained HDAC3 protein from detectable deacetylase activity; tissue/occupancy context.", "limitations": "Recruitment also changes; activity below assay background cannot be excluded and all HDACs are not equivalent." }, { "id": "egelhofer2011", "doi": "10.1038/nsmb.1972", "title": "An assessment of histone-modification antibody quality", "authors": "Egelhofer TA, Minoda A, Klugman S, et al.", "year": 2011, "journal": "Nature Structural & Molecular Biology 18:91–93; online 5 December 2010", "source_type": "primary", "url": "https://doi.org/10.1038/nsmb.1972", "access_depth": "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.", "limitations": "The reported failure fractions describe the tested panel, not all present-day antibodies." }, { "id": "klein2019", "doi": "10.1038/s41593-018-0291-1", "title": "Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains", "authors": "Klein HU, McCabe C, Gjoneska E, et al.", "year": 2019, "journal": "Nature Neuroscience 22:37–46", "source_type": "primary", "url": "https://doi.org/10.1038/s41593-018-0291-1", "access_depth": "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.", "limitations": "Cross-sectional bulk tissue; architecture references from other specimens; model directionality differs from human tissue and raw data were not reanalyzed." }, { "id": "nativio2018", "doi": "10.1038/s41593-018-0101-9", "title": "Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease", "authors": "Nativio R, Donahue G, Berson A, et al.", "year": 2018, "journal": "Nature Neuroscience 21:497–505", "source_type": "primary", "url": "https://doi.org/10.1038/s41593-018-0101-9", "access_depth": "Prior audit original publisher abstract; ledger re-read.", "claim_fit": "H4K16ac comparisons among human temporal-lobe young, elderly cognitively normal and Alzheimer groups.", "limitations": "Abstract-bounded cross-sectional observations; full main Results/covariates and within-person trajectories not appraised." }, { "id": "nativio_notice", "doi": "10.1038/s41593-018-0124-2", "title": "Publisher Correction: Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease", "authors": "Nativio R, Donahue G, Berson A, et al.", "year": 2018, "journal": "Nature Neuroscience", "source_type": "editorial_notice", "url": "https://doi.org/10.1038/s41593-018-0124-2", "access_depth": "Prior audit official publisher correction record and abstract inspected.", "claim_fit": "Corrects Alexandre Amlie-Wolf’s given name; 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publisher body unavailable through web reader.", "claim_fit": "Definitions of membraneless concentration, multivalency and phase separation as an organizing framework.", "limitations": "Foundational framework; specific chromatin mechanisms are supported by primary experiments separately.", "seminal_reason": "Widely used foundational synthesis that established the condensate organizing framework; retained for definitions, not as proof of a particular cellular phase mechanism." }, { "id": "cho2018", "doi": "10.1126/science.aar4199", "title": "Mediator and RNA polymerase II clusters associate in transcription-dependent condensates", "authors": "Cho WK, Spille JH, Hecht M, et al.", "year": 2018, "journal": "Science 361:412–415", "source_type": "primary", "url": "https://doi.org/10.1126/science.aar4199", "access_depth": "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.", "limitations": "Cluster properties support an assembly interpretation but do not uniquely isolate phase separation." }, { "id": "boija2018", "doi": "10.1016/j.cell.2018.10.042", "title": "Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains", "authors": "Boija A, Klein IA, Sabari BR, et al.", "year": 2018, "journal": "Cell 175:1842–1855.e16", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2018.10.042", "access_depth": "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.", "limitations": "Activation-domain mutations can change ordinary coactivator contacts; not a fully phase-selective intervention." }, { "id": "sabari2018", "doi": "10.1126/science.aar3958", "title": "Coactivator condensation at super-enhancers links phase separation and gene control", "authors": "Sabari BR, Dall’Agnese A, Boija A, et al.", "year": 2018, "journal": "Science 361:eaar3958", "source_type": "primary", "url": "https://doi.org/10.1126/science.aar3958", "access_depth": "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.", "limitations": "Abstract-bounded; solvent sensitivity does not alone establish a selective physical mechanism." }, { "id": "chong2018", "doi": "10.1126/science.aar2555", "title": "Imaging dynamic and selective low-complexity domain interactions that control gene transcription", "authors": "Chong S, Dugast-Darzacq C, Liu Z, et al.", "year": 2018, "journal": "Science 361:eaar2555", "source_type": "primary", "url": "https://doi.org/10.1126/science.aar2555", "access_depth": "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.", "limitations": "Study-specific hub regime; not proof against every condensate mechanism." }, { "id": "mcswiggen2019", "doi": "10.7554/eLife.47098", "title": "Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation", "authors": "McSwiggen DT, Hansen AS, Teves SS, et al.", "year": 2019, "journal": "eLife 8:e47098", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.47098", "access_depth": "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.", "limitations": "Viral replication compartment is a mechanistic counterexample, not a replacement model for all host transcription." }, { "id": "guo2019", "doi": "10.1038/s41586-019-1464-0", "title": "Pol II phosphorylation regulates a switch between transcriptional and splicing condensates", "authors": "Guo YE, Manteiga JC, Henninger JE, et al.", "year": 2019, "journal": "Nature 572:543–548", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-019-1464-0", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "CTD phosphorylation-dependent partition between Mediator and splicing-factor condensates.", "limitations": "Biochemical/selected cellular framework; complete path of each polymerase in an intact nucleus not traced." }, { "id": "ctd2024", "doi": "10.1038/s41467-024-52391-6", "title": "Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription", "authors": "Zhang Q, Kim W, Panina SB, Mayfield JE, Portz B, Zhang YJ", "year": 2024, "journal": "Nature Communications 15:7985", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-024-52391-6", "access_depth": "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.", "limitations": "Purified GST-CTD/crowding conditions and pleiotropic CTD variants; functional differences are not automatically phase-exclusive." }, { "id": "henninger2021", "doi": "10.1016/j.cell.2020.11.030", "title": "RNA-Mediated Feedback Control of Transcriptional Condensates", "authors": "Henninger JE, Oksuz O, Shrinivas K, et al.", "year": 2021, "journal": "Cell 184:207–225.e24; online 16 December 2020", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2020.11.030", "access_depth": "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.", "limitations": "Original abstract-bounded qualitative finding; no quantitative RNA threshold or universal bursting rule claimed." }, { "id": "ndf2025", "doi": "10.1038/s41556-025-01778-8", "title": "Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin", "authors": "Li Z, Burgos-Bravo F, Xu K, et al.", "year": 2025, "journal": "Nature Cell Biology 27:1938–1951", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01778-8", "access_depth": "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.", "limitations": "Selected main Results and captions; 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no raw-data reanalysis or independent reproduction of experiments." }, { "id": "ilik", "doi": "10.7554/eLife.60579", "title": "SON and SRRM2 are essential for nuclear speckle formation", "authors": "Ilik et al.", "year": 2020, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.60579", "access_depth": "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", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "sahin", "doi": "10.1083/jcb.201305148", "title": "Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins", "authors": "Sahin et al.", "year": 2014, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201305148", "access_depth": "Scite identity; 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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", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "sloan", "doi": "10.1016/j.celrep.2013.08.049", "title": "The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress", "authors": "Sloan, Bohnsack and Watkins", "year": 2013, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2013.08.049", "access_depth": "Original PMC Summary and selected MDM2/5S RNA interaction Results", "claim_fit": "5S RNP-mediated connection between ribosome biogenesis and p53 regulation.", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "nicoloso", "doi": "10.1006/jmbi.1996.0391", "title": "Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2′-O-ribose methylation of rRNAs", "authors": "Nicoloso et al.", "year": 1996, "journal": "Journal of Molecular Biology", "source_type": "primary", "url": "https://doi.org/10.1006/jmbi.1996.0391", "access_depth": "Primary publication abstract and bibliographic record", "claim_fit": "Fibrillarin-associated nucleolar RNA sequences and guide complementarities; suggested versus demonstrated targets distinguished.", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "yao", "doi": "10.1016/j.molcel.2019.08.014", "title": "Nascent Pre-rRNA Sorting via Phase Separation Drives the Assembly of Dense Fibrillar Components in the Human Nucleolus", "authors": "Yao et al.", "year": 2019, "journal": "Molecular Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2019.08.014", "access_depth": "Scite primary article Highlights/identity; no complete Methods controls accessed", "claim_fit": "Human FC/DFC, nascent pre-rRNA sorting and fibrillarin multivalent clustering; attributed model, no quantitative completeness claim", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." } ], "original_drafts": [ { "path": "Reviews_useredit/Nucleolus_ Cell Biology and Biochemistry.docx", "sha256": "29032ab8040c88bb29fc5014898537704f4d14da6f1b9e2df698eaddb35e4db4" } ] }, { "slug": "nuclear-microrheology", "title": "Nuclear Microrheology: Measuring Local Response in a Living Composite", "subtitle": "From fluorescent tracers to calibrated forces and frequency-dependent mechanics", "group": "biophysics", "html_path": "nuclear_biology_reviews/reviews/nuclear-microrheology-enhanced-graphics.html", "word_path": "Reviews_useredit/current_2026-10-12/nuclear-microrheology.docx", "scientific_words": 2110, "scientific_blocks": 27, "reference_count": 14, "sections": 10, "pages": 8, "html_sha256": "2451d13e693c596f4e14e2ad48f2b8d3a78d114e446cfbf312b360a327811b4f", "word_sha256": "254b53b4b1cb8cbb31d261a679955fe744e428ff2e165afe3aaecf33bdc0a834", "content_sha256": "ed492fcb1e689fb14747d6fd0515af1f0d5956e4b0dbcc2b03393a7ae78c3a96", "parity": { "scientific_blocks_matched": 27, "reference_hyperlinks_matched": 14 }, "source_scope": "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.", "references": [ { "id": "mason", "doi": "10.1103/PhysRevLett.74.1250", "title": "Optical Measurements of Frequency-Dependent Linear Viscoelastic Moduli of Complex Fluids", "authors": "Thomas G. Mason, David A. 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New records lacked complete Scite notice check after monthly quota." }, { "id": "dross", "doi": "10.1371/journal.pone.0005041", "title": "Mapping eGFP Oligomer Mobility in Living Cell Nuclei", "authors": "Nicolas Dross, Corentin Spriet, Monika Zwerger et al.", "year": 2009, "journal": "PLOS ONE", "source_type": "primary", "url": "https://doi.org/10.1371/journal.pone.0005041", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "murade", "doi": "10.1021/acssensors.9b00569", "title": "A Molecular Sensor Reveals Differences in Macromolecular Crowding between the Cytoplasm and Nucleoplasm", "authors": "Chandrashekhar U. Murade, George T. Shubeita", "year": 2019, "journal": "ACS Sensors", "source_type": "primary", "url": "https://doi.org/10.1021/acssensors.9b00569", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "biswas", "doi": "10.1038/s41467-025-62605-0", "title": "Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes", "authors": "Abin Biswas, Omar Muñoz, Kyoohyun Kim et al.", "year": 2025, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-62605-0", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "wei", "doi": "10.1038/s41467-025-66160-6", "title": "Osmotic pressure regulates DNA labelling and transcription with dCas9-SunTag system in live cells", "authors": "Tanlin Wei, Xiaofeng Yang, Chao Jiang et al.", "year": 2025, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-66160-6", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "zhao", "doi": "10.1038/s41467-024-54120-5", "title": "Chromatin compaction during confined cell migration induces and reshapes nuclear condensates", "authors": "Jessica Z. Zhao, Jing Xia, Clifford P. Brangwynne", "year": 2024, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-024-54120-5", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "erdel", "doi": "10.1088/0953-8984/27/6/064115", "title": "The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility", "authors": "Fabian Erdel, Michael Baum, Karsten Rippe", "year": 2015, "journal": "Journal of Physics: Condensed Matter", "source_type": "primary", "url": "https://doi.org/10.1088/0953-8984/27/6/064115", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "rahman", "doi": "10.1038/s41467-025-61358-0", "title": "Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy", "authors": "Fariha Rahman, Victoria Augoustides, Emma Tyler, Timothy A. Daugird, Christian Arthur, Wesley R. Legant", "year": 2025, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-61358-0", "access_depth": "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) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "boersma", "doi": "10.1038/nmeth.3257", "title": "A sensor for quantification of macromolecular crowding in living cells", "authors": "Arnold J. Boersma, Inge S. Zuhorn, Bert Poolman", "year": 2015, "journal": "Nature Methods", "source_type": "primary", "url": "https://doi.org/10.1038/nmeth.3257", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "spoton", "doi": "10.7554/eLife.33125", "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On", "authors": "Anders S. Hansen, Maxime Woringer, Jonathan B. Grimm et al.", "year": 2018, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.33125", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "feric", "doi": "10.1016/j.cell.2016.04.047", "title": "Coexisting Liquid Phases Underlie Nucleolar Subcompartments", "authors": "Marina Feric, Nilesh Vaidya, Tyler S. Harmon et al.", "year": 2016, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2016.04.047", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "rashid", "doi": "10.1016/j.celrep.2024.114462", "title": "Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force", "authors": "Fazlur Rashid, Sadia Amin Kabbo, Ning Wang", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114462", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "byfield", "doi": "10.1016/j.bpj.2024.11.3322", "title": "Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1", "authors": "Fitzroy J. Byfield, Behnaz Eftekhari, Kaeli Kaymak-Loveless et al.", "year": 2025, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1016/j.bpj.2024.11.3322", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." } ], "original_drafts": [] }, { "slug": "nuclear-biophysics", "title": "Nuclear Biophysics: A Decade of Composite Mechanics and Molecular Organization", "subtitle": "Integrated structural, transport and force-based evidence through 2026", "group": "biophysics", "html_path": "nuclear_biology_reviews/reviews/nuclear_biophysics_comprehensive_review.html", "word_path": "Reviews_useredit/current_2026-10-12/nuclear-biophysics.docx", "scientific_words": 2058, "scientific_blocks": 30, "reference_count": 29, "sections": 10, "pages": 9, "html_sha256": "1c831df04764d3521556fb0aa55479de715b5fb4ad3f6e9922b3ef887e24d592", "word_sha256": "562c692d96e29fe17b2cc822a579c805d3b83578e29e7ea2d5a00f456b7b3578", "content_sha256": "c19e56930d641e6899a8c6b9ae5396afcc4e6382730bb2fcc0c6a8608e51f8b4", "parity": { "scientific_blocks_matched": 30, "reference_hyperlinks_matched": 29 }, "source_scope": "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.", "references": [ { "id": "stephens", "doi": "10.1091/mbc.E16-09-0653", "title": "Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus", "authors": "Andrew D. Stephens, Edward J. Banigan, Stephen A. Adam et al.", "year": 2017, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "feric", "doi": "10.1016/j.cell.2016.04.047", "title": "Coexisting Liquid Phases Underlie Nucleolar Subcompartments", "authors": "Marina Feric, Nilesh Vaidya, Tyler S. Harmon et al.", "year": 2016, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2016.04.047", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "denais", "doi": "10.1126/science.aad7297", "title": "Nuclear envelope rupture and repair during cancer cell migration", "authors": "Céline Denais, Rachel M. Gilbert, Philipp Isermann et al.", "year": 2016, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.aad7297", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "rashid", "doi": "10.1016/j.celrep.2024.114462", "title": "Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force", "authors": "Fazlur Rashid, Sadia Amin Kabbo, Ning Wang", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114462", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "byfield", "doi": "10.1016/j.bpj.2024.11.3322", "title": "Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1", "authors": "Fitzroy J. Byfield, Behnaz Eftekhari, Kaeli Kaymak-Loveless et al.", "year": 2025, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1016/j.bpj.2024.11.3322", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "biswas", "doi": "10.1038/s41467-025-62605-0", "title": "Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes", "authors": "Abin Biswas, Omar Muñoz, Kyoohyun Kim et al.", "year": 2025, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-62605-0", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "bergamaschi", "doi": "10.1016/j.celrep.2024.114852", "title": "Heterogeneous force response of chromatin in isolated nuclei.", "authors": "G. Bergamaschi, A. Biebricher, Hannes Witt, F. Byfield, Xamanie M R Seymonson, Cornelis Storm, P. Janmey, G. Wuite", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114852", "access_depth": "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) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "attar", "doi": "10.1093/nar/gkaf763", "title": "Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response", "authors": "A. G. Attar, J. Paturej, Ozan S. Sarıyer, E. Banigan, A. Erbaş", "year": 2025, "journal": "Nucleic Acids Research", "source_type": "primary", "url": "https://doi.org/10.1093/nar/gkaf763", "access_depth": "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) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lewis", "doi": "10.1038/s41556-025-01822-7", "title": "LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis", "authors": "Renard Lewis, Virginia Sinigiani, Noura Maziak et al.", "year": 2026, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01822-7", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "zhao", "doi": "10.1038/s41467-024-54120-5", "title": "Chromatin compaction during confined cell migration induces and reshapes nuclear condensates", "authors": "Jessica Z. Zhao, Jing Xia, Clifford P. Brangwynne", "year": 2024, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-024-54120-5", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "panexm", "doi": "10.1083/jcb.202409120", "title": "Visualizing nuclear pore complex plasticity with pan-expansion microscopy", "authors": "Kimberly J. Morgan, Emma Carley, Alyssa N. Coyne, Jeffrey D. Rothstein, C. Patrick Lusk, Megan C. King", "year": 2025, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.202409120", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "dross", "doi": "10.1371/journal.pone.0005041", "title": "Mapping eGFP Oligomer Mobility in Living Cell Nuclei", "authors": "Nicolas Dross, Corentin Spriet, Monika Zwerger et al.", "year": 2009, "journal": "PLOS ONE", "source_type": "primary", "url": "https://doi.org/10.1371/journal.pone.0005041", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "erdel", "doi": "10.1088/0953-8984/27/6/064115", "title": "The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility", "authors": "Fabian Erdel, Michael Baum, Karsten Rippe", "year": 2015, "journal": "Journal of Physics: Condensed Matter", "source_type": "primary", "url": "https://doi.org/10.1088/0953-8984/27/6/064115", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "turgay", "doi": "10.1038/nature21382", "title": "The molecular architecture of lamins in somatic cells", "authors": "Yagmur Turgay, Matthias Eibauer, Anne E. Goldman et al.", "year": 2017, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature21382", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "linker", "doi": "10.1126/science.abm9798", "title": "Architecture of the linker-scaffold in the nuclear pore", "authors": "Stefan Petrovic, Dipanjan Samanta, Thibaud Perriches et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9798", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "cytoplasmic", "doi": "10.1126/science.abm9129", "title": "Architecture of the cytoplasmic face of the nuclear pore", "authors": "Christopher J. Bley, Si Nie, George W. Mobbs et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9129", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "guelen", "doi": "10.1038/nature06947", "title": "Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2008, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature06947", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "guelen-corr", "doi": "10.1038/nature12316", "title": "Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2013, "journal": "Nature", "source_type": "editorial_notice", "url": "https://doi.org/10.1038/nature12316", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "bancaud", "doi": "10.1038/emboj.2009.340", "title": "Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin", "authors": "Aurélien Bancaud, Sébastien Huet, Nathalie Daigle et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.340", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Tracer exclusion/hindrance and transient chromatin-protein trapping; fractal interpretation remains model dependent.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "frap", "doi": "10.1529/biophysj.103.026765", "title": "Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching", "authors": "Brian L. Sprague, Robert L. Pego, Diana A. Stavreva et al.", "year": 2004, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1529/biophysj.103.026765", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "spoton", "doi": "10.7554/eLife.33125", "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On", "authors": "Anders S. Hansen, Maxime Woringer, Jonathan B. Grimm et al.", "year": 2018, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.33125", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "squires", "doi": "10.1146/annurev-fluid-121108-145608", "title": "Fluid Mechanics of Microrheology", "authors": "Todd M. Squires, Thomas G. Mason", "year": 2010, "journal": "Annual Review of Fluid Mechanics", "source_type": "seminal_review", "url": "https://doi.org/10.1146/annurev-fluid-121108-145608", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.", "seminal_reason": "Foundational review of the physical inference framework underlying particle microrheology, retained for definitions and assumptions rather than claims of nuclear experimental findings." }, { "id": "afm", "doi": "10.1098/rsif.2024.0885", "title": "Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology", "authors": "Ellen Juel Pørtner, Anna Mularski, Tobias William Jarrett, Stine Lauritzen Sønder, Jesper Nylandsted, Adam Cohen Simonsen", "year": 2025, "journal": "Journal of the Royal Society Interface", "source_type": "primary", "url": "https://doi.org/10.1098/rsif.2024.0885", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "linc", "doi": "10.1083/jcb.200509124", "title": "Coupling of the nucleus and cytoplasm: role of the LINC complex", "authors": "Melissa Crisp, Qian Liu, Kyle Roux et al.", "year": 2006, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.200509124", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "yap", "doi": "10.1016/j.cell.2017.10.008", "title": "Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores", "authors": "Alberto Elosegui-Artola, Ion Andreu, Amy E. M. Beedle et al.", "year": 2017, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2017.10.008", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "olmos", "doi": "10.1038/nature14503", "title": "ESCRT-III controls nuclear envelope reformation", "authors": "Yolanda Olmos, Lorna Hodgson, Judith Mantell, Paul Verkade, Jeremy G. Carlton", "year": 2015, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature14503", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "hoffmann", "doi": "10.1016/j.molcel.2024.11.038", "title": "Nuclear pore permeability and fluid flow are modulated by its dilation state", "authors": "Patrick C. Hoffmann, Hyuntae Kim, Aleksandra Obarska-Kosińska et al.", "year": 2024, "journal": "Molecular Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2024.11.038", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "timney", "doi": "10.1083/jcb.201601004", "title": "Simple rules for passive diffusion through the nuclear pore complex", "authors": "Benjamin L. Timney, Barak Raveh, Roxana Mironska et al.", "year": 2016, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201601004", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "mccreery", "doi": "10.1038/s41556-025-01767-x", "title": "Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells", "authors": "Kaitlin P. McCreery, Aki Stubb, Rebecca Stephens et al.", "year": 2025, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01767-x", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." } ], "original_drafts": [ { "path": "Reviews_useredit/Nuclear Biophysics_ Recent Decade Review_.docx", "sha256": "3054b919e7a1e2ca419f4a10c937b67ececab84c01935420713b7cf518d5048a" } ] }, { "slug": "nuclear-envelope", "title": "The Nuclear Envelope: Membranes, Genome Coupling and Regulated Remodeling", "subtitle": "A complete current synthesis of boundary structure and function", "group": "biophysics", "html_path": "nuclear_biology_reviews/reviews/nuclear-envelope-comprehensive-review.html", "word_path": "Reviews_useredit/current_2026-10-12/nuclear-envelope.docx", "scientific_words": 2045, "scientific_blocks": 29, "reference_count": 23, "sections": 10, "pages": 9, "html_sha256": "923d9ee49ae63b435a4cea75588470bf6567fbcdff7be5a0b01d2bd17fc95eec", "word_sha256": "85b03919a3586288ef0c8e927a328fcc0a9a8a1482d06c31508f83a57a1d86e0", "content_sha256": "0320486b5268d75fb58c4fd5a055f90883ce13c90c67dcef7121d16d26d3cb95", "parity": { "scientific_blocks_matched": 29, "reference_hyperlinks_matched": 23 }, "source_scope": "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.", "references": [ { "id": "linc", "doi": "10.1083/jcb.200509124", "title": "Coupling of the nucleus and cytoplasm: role of the LINC complex", "authors": "Melissa Crisp, Qian Liu, Kyle Roux et al.", "year": 2006, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.200509124", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "eibauer", "doi": "10.1038/ncomms8532", "title": "Structure and gating of the nuclear pore complex", "authors": "Matthias Eibauer, Mauro Pellanda, Yagmur Turgay et al.", "year": 2015, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/ncomms8532", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "ran", "doi": "10.1093/emboj/16.21.6535", "title": "The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus", "authors": "Elisa Izaurralde, Ulrike Kutay, Cayetano von Kobbe et al.", "year": 1997, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1093/emboj/16.21.6535", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "osutsumi", "doi": "10.7554/eLife.19071", "title": "Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope", "authors": "Shotaro Otsuka, Khanh Huy Bui, Martin Schorb et al.", "year": 2016, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.19071", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "olmos", "doi": "10.1038/nature14503", "title": "ESCRT-III controls nuclear envelope reformation", "authors": "Yolanda Olmos, Lorna Hodgson, Judith Mantell, Paul Verkade, Jeremy G. Carlton", "year": 2015, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature14503", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "denais", "doi": "10.1126/science.aad7297", "title": "Nuclear envelope rupture and repair during cancer cell migration", "authors": "Céline Denais, Rachel M. Gilbert, Philipp Isermann et al.", "year": 2016, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.aad7297", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lewis", "doi": "10.1038/s41556-025-01822-7", "title": "LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis", "authors": "Renard Lewis, Virginia Sinigiani, Noura Maziak et al.", "year": 2026, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01822-7", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "panexm", "doi": "10.1083/jcb.202409120", "title": "Visualizing nuclear pore complex plasticity with pan-expansion microscopy", "authors": "Kimberly J. Morgan, Emma Carley, Alyssa N. Coyne, Jeffrey D. Rothstein, C. Patrick Lusk, Megan C. King", "year": 2025, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.202409120", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "hoffmann", "doi": "10.1016/j.molcel.2024.11.038", "title": "Nuclear pore permeability and fluid flow are modulated by its dilation state", "authors": "Patrick C. Hoffmann, Hyuntae Kim, Aleksandra Obarska-Kosińska et al.", "year": 2024, "journal": "Molecular Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2024.11.038", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "attar", "doi": "10.1093/nar/gkaf763", "title": "Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response", "authors": "A. G. Attar, J. Paturej, Ozan S. Sarıyer, E. Banigan, A. Erbaş", "year": 2025, "journal": "Nucleic Acids Research", "source_type": "primary", "url": "https://doi.org/10.1093/nar/gkaf763", "access_depth": "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) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "biswas", "doi": "10.1038/s41467-025-62605-0", "title": "Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes", "authors": "Abin Biswas, Omar Muñoz, Kyoohyun Kim et al.", "year": 2025, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-62605-0", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "turgay", "doi": "10.1038/nature21382", "title": "The molecular architecture of lamins in somatic cells", "authors": "Yagmur Turgay, Matthias Eibauer, Anne E. Goldman et al.", "year": 2017, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature21382", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "linker", "doi": "10.1126/science.abm9798", "title": "Architecture of the linker-scaffold in the nuclear pore", "authors": "Stefan Petrovic, Dipanjan Samanta, Thibaud Perriches et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9798", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "timney", "doi": "10.1083/jcb.201601004", "title": "Simple rules for passive diffusion through the nuclear pore complex", "authors": "Benjamin L. Timney, Barak Raveh, Roxana Mironska et al.", "year": 2016, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201601004", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "mohr", "doi": "10.1038/emboj.2009.200", "title": "Characterisation of the passive permeability barrier of nuclear pore complexes", "authors": "Dagmar Mohr, Steffen Frey, Torsten Fischer et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.200", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dbp5", "doi": "10.1101/gad.2040611", "title": "The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1", "authors": "Kristen N. Noble, Elizabeth Tran, Abel R. Alcázar-Román et al.", "year": 2011, "journal": "Genes & Development", "source_type": "primary", "url": "https://doi.org/10.1101/gad.2040611", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Nup159/Gle1-IP6 regulation of Dbp5 nucleotide/remodeling cycles; distinct from general Ran-mediated traffic.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "cytoplasmic", "doi": "10.1126/science.abm9129", "title": "Architecture of the cytoplasmic face of the nuclear pore", "authors": "Christopher J. Bley, Si Nie, George W. Mobbs et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9129", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lem2", "doi": "10.1038/s41586-020-2232-x", "title": "LEM2 phase separation governs ESCRT-mediated nuclear envelope reformation", "authors": "Alexander von Appen, Dollie LaJoie, Isabel E. Johnson et al.", "year": 2020, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-020-2232-x", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "guelen", "doi": "10.1038/nature06947", "title": "Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2008, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature06947", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "guelen-corr", "doi": "10.1038/nature12316", "title": "Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2013, "journal": "Nature", "source_type": "editorial_notice", "url": "https://doi.org/10.1038/nature12316", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lammerding", "doi": "10.1172/JCI19670", "title": "Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction", "authors": "Jan Lammerding, Paul Christian Schulze, Tomosaburo Takahashi et al.", "year": 2004, "journal": "Journal of Clinical Investigation", "source_type": "primary", "url": "https://doi.org/10.1172/JCI19670", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "stephens", "doi": "10.1091/mbc.E16-09-0653", "title": "Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus", "authors": "Andrew D. Stephens, Edward J. Banigan, Stephen A. Adam et al.", "year": 2017, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dangelo", "doi": "10.1016/j.cell.2008.11.037", "title": "Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells", "authors": "Maximiliano A. D’Angelo, Marcela Raı́ces, Siler H. Panowski et al.", "year": 2009, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2008.11.037", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." } ], "original_drafts": [ { "path": "Reviews_useredit/Nuclear Envelope_ Structure and Dynamics.docx", "sha256": "a2fa0be8b431ce727db6b522667d80a81981bce24a4ebc3ff3f53c72a9793c1c" } ] }, { "slug": "nuclear-lamina", "title": "The Nuclear Lamina: Filament Architecture, Genome Attachment and Cell Function", "subtitle": "A current synthesis of structural, mechanical and genetic evidence", "group": "biophysics", "html_path": "nuclear_biology_reviews/reviews/nuclear-lamina-comprehensive-review.html", "word_path": "Reviews_useredit/current_2026-10-12/nuclear-lamina.docx", "scientific_words": 2042, "scientific_blocks": 29, "reference_count": 15, "sections": 10, "pages": 8, "html_sha256": "64a910e7e0839cf6691f27ae3c07b00266739c111b28bbccd978cc5aeffaf05f", "word_sha256": "ef7bd9fe398781ddbf5aeb7432a5201d994c76e3ec8a22186f982b76d5853b7c", "content_sha256": "dd58c14a6d99c3f8215e6f1532403270990576ee03d745e756f521edbdeeb82a", "parity": { "scientific_blocks_matched": 29, "reference_hyperlinks_matched": 15 }, "source_scope": "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.", "references": [ { "id": "turgay", "doi": "10.1038/nature21382", "title": "The molecular architecture of lamins in somatic cells", "authors": "Yagmur Turgay, Matthias Eibauer, Anne E. Goldman et al.", "year": 2017, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature21382", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "guelen", "doi": "10.1038/nature06947", "title": "Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2008, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature06947", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "stephens", "doi": "10.1091/mbc.E16-09-0653", "title": "Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus", "authors": "Andrew D. Stephens, Edward J. Banigan, Stephen A. Adam et al.", "year": 2017, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "bonne", "doi": "10.1038/6799", "title": "Mutations in the gene encoding lamin A/C cause autosomal dominant Emery-Dreifuss muscular dystrophy", "authors": "Gisèle Bonne, Marina Raffaele di Barletta, Shaïda Varnous et al.", "year": 1999, "journal": "Nature Genetics", "source_type": "primary", "url": "https://doi.org/10.1038/6799", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "eriksson", "doi": "10.1038/nature01629", "title": "Recurrent de novo point mutations in lamin A cause Hutchinson–Gilford progeria syndrome", "authors": "Maria Eriksson, William Ted Brown, Leslie B. Gordon et al.", "year": 2003, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature01629", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lewis", "doi": "10.1038/s41556-025-01822-7", "title": "LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis", "authors": "Renard Lewis, Virginia Sinigiani, Noura Maziak et al.", "year": 2026, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01822-7", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "attar", "doi": "10.1093/nar/gkaf763", "title": "Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response", "authors": "A. G. Attar, J. Paturej, Ozan S. Sarıyer, E. Banigan, A. Erbaş", "year": 2025, "journal": "Nucleic Acids Research", "source_type": "primary", "url": "https://doi.org/10.1093/nar/gkaf763", "access_depth": "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) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lammerding", "doi": "10.1172/JCI19670", "title": "Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction", "authors": "Jan Lammerding, Paul Christian Schulze, Tomosaburo Takahashi et al.", "year": 2004, "journal": "Journal of Clinical Investigation", "source_type": "primary", "url": "https://doi.org/10.1172/JCI19670", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "freund", "doi": "10.1091/mbc.E11-10-0884", "title": "Lamin B1 loss is a senescence-associated biomarker", "authors": "Adam Freund, Rémi-Martin Laberge, Marco Demaria et al.", "year": 2012, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E11-10-0884", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "linc", "doi": "10.1083/jcb.200509124", "title": "Coupling of the nucleus and cytoplasm: role of the LINC complex", "authors": "Melissa Crisp, Qian Liu, Kyle Roux et al.", "year": 2006, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.200509124", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "guelen-corr", "doi": "10.1038/nature12316", "title": "Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2013, "journal": "Nature", "source_type": "editorial_notice", "url": "https://doi.org/10.1038/nature12316", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "bergamaschi", "doi": "10.1016/j.celrep.2024.114852", "title": "Heterogeneous force response of chromatin in isolated nuclei.", "authors": "G. Bergamaschi, A. Biebricher, Hannes Witt, F. Byfield, Xamanie M R Seymonson, Cornelis Storm, P. Janmey, G. Wuite", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114852", "access_depth": "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) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "byfield", "doi": "10.1016/j.bpj.2024.11.3322", "title": "Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1", "authors": "Fitzroy J. Byfield, Behnaz Eftekhari, Kaeli Kaymak-Loveless et al.", "year": 2025, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1016/j.bpj.2024.11.3322", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "afm", "doi": "10.1098/rsif.2024.0885", "title": "Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology", "authors": "Ellen Juel Pørtner, Anna Mularski, Tobias William Jarrett, Stine Lauritzen Sønder, Jesper Nylandsted, Adam Cohen Simonsen", "year": 2025, "journal": "Journal of the Royal Society Interface", "source_type": "primary", "url": "https://doi.org/10.1098/rsif.2024.0885", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "denais", "doi": "10.1126/science.aad7297", "title": "Nuclear envelope rupture and repair during cancer cell migration", "authors": "Céline Denais, Rachel M. Gilbert, Philipp Isermann et al.", "year": 2016, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.aad7297", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." } ], "original_drafts": [ { "path": "Reviews_useredit/Lamina_ Structure, Function, and Disease_.docx", "sha256": "74208dc68151f7f406adc2fc0105b978360085005cfc63669f231908abed94cc" } ] }, { "slug": "nuclear-pore-complex", "title": "Nuclear Pore Complexes: Architecture, Selective Transport and Plasticity", "subtitle": "Integrated primary evidence from structural scaffolds to current barrier dynamics", "group": "biophysics", "html_path": "nuclear_biology_reviews/reviews/nuclear_pore_complex_standardized_review.html", "word_path": "Reviews_useredit/current_2026-10-12/nuclear-pore-complex.docx", "scientific_words": 2039, "scientific_blocks": 31, "reference_count": 19, "sections": 10, "pages": 8, "html_sha256": "f071433f7bef66651399dbe9d061ed045fa7d8deeea0dd353e3cc1ea79b29b95", "word_sha256": "460fa52eb3d57fecd799c387afd2a90ed1a3b4bd7c1a47c7116f22e2f8d9ec90", "content_sha256": "5f9dfaf820193c110f43bfa8e6792f4d6c66295de872bb0d8c49282a74ebeaeb", "parity": { "scientific_blocks_matched": 31, "reference_hyperlinks_matched": 19 }, "source_scope": "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.", "references": [ { "id": "linker", "doi": "10.1126/science.abm9798", "title": "Architecture of the linker-scaffold in the nuclear pore", "authors": "Stefan Petrovic, Dipanjan Samanta, Thibaud Perriches et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9798", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "cytoplasmic", "doi": "10.1126/science.abm9129", "title": "Architecture of the cytoplasmic face of the nuclear pore", "authors": "Christopher J. Bley, Si Nie, George W. Mobbs et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9129", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "timney", "doi": "10.1083/jcb.201601004", "title": "Simple rules for passive diffusion through the nuclear pore complex", "authors": "Benjamin L. Timney, Barak Raveh, Roxana Mironska et al.", "year": 2016, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201601004", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "ran", "doi": "10.1093/emboj/16.21.6535", "title": "The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus", "authors": "Elisa Izaurralde, Ulrike Kutay, Cayetano von Kobbe et al.", "year": 1997, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1093/emboj/16.21.6535", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dbp5", "doi": "10.1101/gad.2040611", "title": "The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1", "authors": "Kristen N. Noble, Elizabeth Tran, Abel R. Alcázar-Román et al.", "year": 2011, "journal": "Genes & Development", "source_type": "primary", "url": "https://doi.org/10.1101/gad.2040611", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Nup159/Gle1-IP6 regulation of Dbp5 nucleotide/remodeling cycles; distinct from general Ran-mediated traffic.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "hoffmann", "doi": "10.1016/j.molcel.2024.11.038", "title": "Nuclear pore permeability and fluid flow are modulated by its dilation state", "authors": "Patrick C. Hoffmann, Hyuntae Kim, Aleksandra Obarska-Kosińska et al.", "year": 2024, "journal": "Molecular Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2024.11.038", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "panexm", "doi": "10.1083/jcb.202409120", "title": "Visualizing nuclear pore complex plasticity with pan-expansion microscopy", "authors": "Kimberly J. Morgan, Emma Carley, Alyssa N. Coyne, Jeffrey D. Rothstein, C. Patrick Lusk, Megan C. King", "year": 2025, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.202409120", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "kozai", "doi": "10.1038/s41556-025-01812-9", "title": "Karyopherins remodel the dynamic organization of the nuclear pore complex transport barrier", "authors": "Toshiya Kozai, Javier Fernandez-Martinez, Larisa E. Kapinos et al.", "year": 2025, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01812-9", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "eibauer", "doi": "10.1038/ncomms8532", "title": "Structure and gating of the nuclear pore complex", "authors": "Matthias Eibauer, Mauro Pellanda, Yagmur Turgay et al.", "year": 2015, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/ncomms8532", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dickson", "doi": "10.1038/s41586-023-06969-7", "title": "The HIV capsid mimics karyopherin engagement of FG-nucleoporins", "authors": "Claire F. Dickson, Sophie Hertel, Andrew Tuckwell et al.", "year": 2024, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-023-06969-7", "access_depth": "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) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "stoichiometry", "doi": "10.1038/msb.2013.4", "title": "Cell type‐specific nuclear pores: a case in point for context‐dependent stoichiometry of molecular machines", "authors": "Alessandro Ori‬‬, Niccolò Banterle, Murat Iskar et al.", "year": 2013, "journal": "Molecular Systems Biology", "source_type": "primary", "url": "https://doi.org/10.1038/msb.2013.4", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dangelo", "doi": "10.1016/j.cell.2008.11.037", "title": "Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells", "authors": "Maximiliano A. D’Angelo, Marcela Raı́ces, Siler H. Panowski et al.", "year": 2009, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2008.11.037", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "mohr", "doi": "10.1038/emboj.2009.200", "title": "Characterisation of the passive permeability barrier of nuclear pore complexes", "authors": "Dagmar Mohr, Steffen Frey, Torsten Fischer et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.200", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "osutsumi", "doi": "10.7554/eLife.19071", "title": "Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope", "authors": "Shotaro Otsuka, Khanh Huy Bui, Martin Schorb et al.", "year": 2016, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.19071", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "olmos", "doi": "10.1038/nature14503", "title": "ESCRT-III controls nuclear envelope reformation", "authors": "Yolanda Olmos, Lorna Hodgson, Judith Mantell, Paul Verkade, Jeremy G. Carlton", "year": 2015, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature14503", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "lem2", "doi": "10.1038/s41586-020-2232-x", "title": "LEM2 phase separation governs ESCRT-mediated nuclear envelope reformation", "authors": "Alexander von Appen, Dollie LaJoie, Isabel E. Johnson et al.", "year": 2020, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-020-2232-x", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "yap", "doi": "10.1016/j.cell.2017.10.008", "title": "Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores", "authors": "Alberto Elosegui-Artola, Ion Andreu, Amy E. M. Beedle et al.", "year": 2017, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2017.10.008", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "biswas", "doi": "10.1038/s41467-025-62605-0", "title": "Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes", "authors": "Abin Biswas, Omar Muñoz, Kyoohyun Kim et al.", "year": 2025, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-62605-0", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "denais", "doi": "10.1126/science.aad7297", "title": "Nuclear envelope rupture and repair during cancer cell migration", "authors": "Céline Denais, Rachel M. Gilbert, Philipp Isermann et al.", "year": 2016, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.aad7297", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." } ], "original_drafts": [ { "path": "Reviews_useredit/Nuclear Pore Complex Comprehensive Review.docx", "sha256": "a29bdf1ed4d53e5dcb7bbb874dfa6d25e5dd2d46ee00a78e6a77d5ec9e39b6b5" } ] }, { "slug": "nuclear-transport", "title": "Nuclear Transport and Compartment Dynamics: Gates, Search and Processing", "subtitle": "A unified review that preserves the distinction between boundary exchange and internal movement", "group": "biophysics", "html_path": "nuclear_biology_reviews/reviews/nuclear-transport-compartment-dynamics.html", "word_path": "Reviews_useredit/current_2026-10-12/nuclear-transport.docx", "scientific_words": 2038, "scientific_blocks": 30, "reference_count": 17, "sections": 10, "pages": 8, "html_sha256": "3973208d80d8c312a784d402801f53d67c2bda7961bcc8a14d0a21866dff8d34", "word_sha256": "e93f36a2d70b469f6b8fbe15623d5069548dabee4dc07e826c18ffca453fc0f0", "content_sha256": "9b63102e11c8c78795740f58254d40b4ca13b084857f9a15e49172485e6e50f7", "parity": { "scientific_blocks_matched": 30, "reference_hyperlinks_matched": 17 }, "source_scope": "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.", "references": [ { "id": "timney", "doi": "10.1083/jcb.201601004", "title": "Simple rules for passive diffusion through the nuclear pore complex", "authors": "Benjamin L. Timney, Barak Raveh, Roxana Mironska et al.", "year": 2016, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201601004", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "ran", "doi": "10.1093/emboj/16.21.6535", "title": "The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus", "authors": "Elisa Izaurralde, Ulrike Kutay, Cayetano von Kobbe et al.", "year": 1997, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1093/emboj/16.21.6535", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dbp5", "doi": "10.1101/gad.2040611", "title": "The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1", "authors": "Kristen N. Noble, Elizabeth Tran, Abel R. Alcázar-Román et al.", "year": 2011, "journal": "Genes & Development", "source_type": "primary", "url": "https://doi.org/10.1101/gad.2040611", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Nup159/Gle1-IP6 regulation of Dbp5 nucleotide/remodeling cycles; distinct from general Ran-mediated traffic.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dross", "doi": "10.1371/journal.pone.0005041", "title": "Mapping eGFP Oligomer Mobility in Living Cell Nuclei", "authors": "Nicolas Dross, Corentin Spriet, Monika Zwerger et al.", "year": 2009, "journal": "PLOS ONE", "source_type": "primary", "url": "https://doi.org/10.1371/journal.pone.0005041", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "frap", "doi": "10.1529/biophysj.103.026765", "title": "Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching", "authors": "Brian L. Sprague, Robert L. Pego, Diana A. Stavreva et al.", "year": 2004, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1529/biophysj.103.026765", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "feric", "doi": "10.1016/j.cell.2016.04.047", "title": "Coexisting Liquid Phases Underlie Nucleolar Subcompartments", "authors": "Marina Feric, Nilesh Vaidya, Tyler S. Harmon et al.", "year": 2016, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2016.04.047", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "quinodoz", "doi": "10.1038/s41586-025-09207-4", "title": "Mapping and engineering RNA-driven architecture of the multiphase nucleolus", "authors": "Sofia A. Quinodoz, Lifei Jiang, Aya A. Abu-Alfa et al.", "year": 2025, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-025-09207-4", "access_depth": "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) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "kozai", "doi": "10.1038/s41556-025-01812-9", "title": "Karyopherins remodel the dynamic organization of the nuclear pore complex transport barrier", "authors": "Toshiya Kozai, Javier Fernandez-Martinez, Larisa E. Kapinos et al.", "year": 2025, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01812-9", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "hoffmann", "doi": "10.1016/j.molcel.2024.11.038", "title": "Nuclear pore permeability and fluid flow are modulated by its dilation state", "authors": "Patrick C. Hoffmann, Hyuntae Kim, Aleksandra Obarska-Kosińska et al.", "year": 2024, "journal": "Molecular Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2024.11.038", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "biswas", "doi": "10.1038/s41467-025-62605-0", "title": "Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes", "authors": "Abin Biswas, Omar Muñoz, Kyoohyun Kim et al.", "year": 2025, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-62605-0", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "mohr", "doi": "10.1038/emboj.2009.200", "title": "Characterisation of the passive permeability barrier of nuclear pore complexes", "authors": "Dagmar Mohr, Steffen Frey, Torsten Fischer et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.200", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "erdel", "doi": "10.1088/0953-8984/27/6/064115", "title": "The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility", "authors": "Fabian Erdel, Michael Baum, Karsten Rippe", "year": 2015, "journal": "Journal of Physics: Condensed Matter", "source_type": "primary", "url": "https://doi.org/10.1088/0953-8984/27/6/064115", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "bancaud", "doi": "10.1038/emboj.2009.340", "title": "Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin", "authors": "Aurélien Bancaud, Sébastien Huet, Nathalie Daigle et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.340", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Tracer exclusion/hindrance and transient chromatin-protein trapping; fractal interpretation remains model dependent.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "spoton", "doi": "10.7554/eLife.33125", "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On", "authors": "Anders S. Hansen, Maxime Woringer, Jonathan B. Grimm et al.", "year": 2018, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.33125", "access_depth": "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.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "yap", "doi": "10.1016/j.cell.2017.10.008", "title": "Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores", "authors": "Alberto Elosegui-Artola, Ion Andreu, Amy E. M. Beedle et al.", "year": 2017, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2017.10.008", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "rashid", "doi": "10.1016/j.celrep.2024.114462", "title": "Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force", "authors": "Fazlur Rashid, Sadia Amin Kabbo, Ning Wang", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114462", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "panexm", "doi": "10.1083/jcb.202409120", "title": "Visualizing nuclear pore complex plasticity with pan-expansion microscopy", "authors": "Kimberly J. Morgan, Emma Carley, Alyssa N. Coyne, Jeffrey D. Rothstein, C. Patrick Lusk, Megan C. King", "year": 2025, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.202409120", "access_depth": "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.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." } ], "original_drafts": [] } ] }