Shin Y, Brangwynne CP. Liquid phase condensation in cell physiology and disease. Science. 2017;357(6357):eaaf4382.
Article
PubMed
CAS
Google Scholar
Banani SF, Lee HO, Hyman AA, Rosen MK. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol. 2017;18(5):285–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hyman AA, Weber CA, Julicher F. Liquid-liquid phase separation in biology. Annu Rev Cell Dev Biol. 2014;30(1):39–58.
Article
CAS
PubMed
Google Scholar
Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, Schymkowitz J, Shorter J, Wolozin B, Van Den Bosch L, et al. Protein phase separation: a new phase in cell biology. Trends Cell Biol. 2018;28(6):420–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Toretsky JA, Wright PE. Assemblages: functional units formed by cellular phase separation assemblage: phase separations in cells. J Cell Biol. 2014;206(5):579–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altmeyer M, Neelsen KJ, Teloni F, Pozdnyakova I, Pellegrino S, Grofte M, Rask MD, Streicher W, Jungmichel S, Nielsen ML, et al. Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose). Nat Commun. 2015;6:8088.
Article
CAS
PubMed
Google Scholar
Zhu L, Brangwynne CP. Nuclear bodies: the emerging biophysics of nucleoplasmic phases. Curr Opin Cell Biol. 2015;34:23–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Uversky VN. Intrinsically disordered proteins in overcrowded milieu: membrane-less organelles, phase separation, and intrinsic disorder. Curr Opin Struct Biol. 2017;44:18–30.
Article
CAS
PubMed
Google Scholar
Oth A, Desreux V. Soluibilte et dissociation d’une desoxyribonucleoproteine. J Polym Sci. 1957;23:73–6.
Article
Google Scholar
Jensen RH, Chalkley R. The physical state of nucleohistone under physiological ionic strength. The effect of interaction with free nucleic acids. Biochemistry. 1968;7(12):4388–95.
Article
CAS
PubMed
Google Scholar
Marushige K, Bonner J. Fractionation of liver chromatin. Proc Natl Acad Sci USA. 1971;68(12):2941–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gottesfeld JM, Garrard WT, Bagi G, Wilson RF, Bonner J. Partial purification of the template-active fraction of chromatin: a preliminary report. Proc Natl Acad Sci USA. 1974;71(6):2193–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davie JR, Candido EP. Acetylated histone H4 is preferentially associated with template-active chromatin. Proc Natl Acad Sci USA. 1978;75(8):3574–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perry M, Chalkley R. The effect of histone hyperacetylation on the nuclease sensitivity and the solubility of chromatin. J Biol Chem. 1981;256(7):3313–8.
Article
CAS
PubMed
Google Scholar
Rocha E, Davie JR, van Holde KE, Weintraub H. Differential salt fractionation of active and inactive genomic domains in chicken erythrocyte. J Biol Chem. 1984;259(13):8558–63.
Article
CAS
PubMed
Google Scholar
Sanders MM. Fractionation of nucleosomes by salt elution from micrococcal nuclease-digested nuclei. J Cell Biol. 1978;79(1):97–109.
Article
CAS
PubMed
Google Scholar
Henikoff S, Henikoff JG, Sakai A, Loeb GB, Ahmad K. Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Res. 2009;19(3):460–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Teves SS, Henikoff S. Salt fractionation of nucleosomes for genome-wide profiling. Methods Mol Biol. 2012;833:421–32.
Article
CAS
PubMed
Google Scholar
Thakur J, Henikoff S. Unexpected conformational variations of the human centromeric chromatin complex. Genes Dev. 2018;32(1):20–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Finch JT, Klug A. Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA. 1976;73(6):1897–901.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hansen JC. Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. Annu Rev Biophys Biomol Struct. 2002;31(1):361–92.
Article
CAS
PubMed
Google Scholar
Thoma F, Koller T, Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol. 1979;83(2 Pt 1):403–27.
Article
CAS
PubMed
Google Scholar
Simpson RT, Thoma F, Brubaker JM. Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell. 1985;42(3):799–808.
Article
CAS
PubMed
Google Scholar
Hansen JC, Ausio J, Stanik VH, van Holde KE. Homogeneous reconstituted oligonucleosomes, evidence for salt-dependent folding in the absence of histone H1. Biochemistry. 1989;28(23):9129–36.
Article
CAS
PubMed
Google Scholar
Garcia-Ramirez M, Dong F, Ausio J. Role of the histone “tails” in the folding of oligonucleosomes depleted of histone H1. J Biol Chem. 1992;267(27):19587–95.
Article
CAS
PubMed
Google Scholar
Schwarz PM, Hansen JC. Formation and stability of higher order chromatin structures. Contributions of the histone octamer. J Biol Chem. 1994;269(23):16284–9.
Article
CAS
PubMed
Google Scholar
Schwarz PM, Felthauser A, Fletcher TM, Hansen JC. Reversible oligonucleosome self-association: dependence on divalent cations and core histone tail domains. Biochemistry. 1996;35(13):4009–15.
Article
CAS
PubMed
Google Scholar
Tse C, Sera T, Wolffe AP, Hansen JC. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol. 1998;18(8):4629–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carruthers LM, Bednar J, Woodcock CL, Hansen JC. Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: mechanistic ramifications for higher-order chromatin folding. Biochemistry. 1998;37(42):14776–87.
Article
CAS
PubMed
Google Scholar
Perry M, Chalkley R. Histone acetylation increases the solubility of chromatin and occurs sequentially over most of the chromatin. A novel model for the biological role of histone acetylation. J Biol Chem. 1982;257(13):7336–47.
Article
CAS
PubMed
Google Scholar
Hendzel MJ, Delcuve GP, Davie JR. Histone deacetylase is a component of the internal nuclear matrix. J Biol Chem. 1991;266(32):21936–42.
Article
CAS
PubMed
Google Scholar
Zhou J, Fan JY, Rangasamy D, Tremethick DJ. The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression. Nat Struct Mol Biol. 2007;14(11):1070–6.
Article
CAS
PubMed
Google Scholar
Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N, Henry L, Gerlich DW, Redding S, Rosen MK. Organization of chromatin by intrinsic and regulated phase separation. Cell. 2019;179(2):470–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maeshima K, Rogge R, Tamura S, Joti Y, Hikima T, Szerlong H, Krause C, Herman J, Seidel E, DeLuca J, et al. Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers. EMBO J. 2016;35(10):1115–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Strickfaden H, Tolsma TO, Sharma A, Underhill DA, Hansen JC, Hendzel MJ. Condensed chromatin behaves like a solid on the mesoscale in vitro and in living cells. Cell. 2020;183(7):1772–84.
Article
CAS
PubMed
Google Scholar
Dorigo B, Schalch T, Bystricky K, Richmond TJ. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol. 2003;327(1):85–96.
Article
CAS
PubMed
Google Scholar
Brosey CA, Tainer JA. Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Curr Opin Struct Biol. 2019;58:197–213.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maeshima K, Imai R, Hikima T, Joti Y. Chromatin structure revealed by X-ray scattering analysis and computational modeling. Methods. 2014;70(2–3):154–61.
Article
CAS
PubMed
Google Scholar
Korolev N, Allahverdi A, Lyubartsev AP, Nordenskiold L. The polyelectrolyte properties of chromatin. Soft Matter. 2012;8:9322–33.
Article
CAS
Google Scholar
Gordon F, Luger K, Hansen JC. The core histone N-terminal tail domains function independently and additively during salt-dependent oligomerization of nucleosomal arrays. J Biol Chem. 2005;280(40):33701–6.
Article
CAS
PubMed
Google Scholar
McBryant SJ, Klonoski J, Sorensen TC, Norskog SS, Williams S, Resch MG, Toombs JA 3rd, Hobdey SE, Hansen JC. Determinants of histone H4 N-terminal domain function during nucleosomal array oligomerization: roles of amino acid sequence, domain length, and charge density. J Biol Chem. 2009;284(25):16716–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kan PY, Caterino TL, Hayes JJ. The H4 tail domain participates in intra- and internucleosome interactions with protein and DNA during folding and oligomerization of nucleosome arrays. Mol Cell Biol. 2009;29(2):538–46.
Article
CAS
PubMed
Google Scholar
Kan PY, Hayes JJ. Detection of interactions between nucleosome arrays mediated by specific core histone tail domains. Methods. 2007;41(3):278–85.
Article
CAS
PubMed
Google Scholar
Zheng C, Lu X, Hansen JC, Hayes JJ. Salt-dependent intra- and internucleosomal interactions of the H3 tail domain in a model oligonucleosomal array. J Biol Chem. 2005;280(39):33552–7.
Article
CAS
PubMed
Google Scholar
Pepenella S, Murphy KJ, Hayes JJ. A distinct switch in interactions of the histone H4 tail domain upon salt-dependent folding of nucleosome arrays. J Biol Chem. 2014;289(39):27342–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hong L, Schroth GP, Matthews HR, Yau P, Bradbury EM. Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA. J Biol Chem. 1993;268(1):305–14.
Article
CAS
PubMed
Google Scholar
Allahverdi A, Yang R, Korolev N, Fan Y, Davey CA, Liu CF, Nordenskiold L. The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association. Nucleic Acids Res. 2011;39(5):1680–91.
Article
CAS
PubMed
Google Scholar
Dhall A, Wei S, Fierz B, Woodcock CL, Lee TH, Chatterjee C. Sumoylated human histone H4 prevents chromatin compaction by inhibiting long-range internucleosomal interactions. J Biol Chem. 2014;289(49):33827–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL. Histone H4–K16 acetylation controls chromatin structure and protein interactions. Science. 2006;311(5762):844–7.
Article
CAS
PubMed
Google Scholar
Mishra LN, Pepenella S, Rogge R, Hansen JC, Hayes JJ. Acetylation mimics within a single nucleosome alter local DNA accessibility in compacted nucleosome arrays. Sci Rep. 2016;6:34808.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fierz B, Chatterjee C, McGinty RK, Bar-Dagan M, Raleigh DP, Muir TW. Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat Chem Biol. 2011;7(2):113–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Debelouchina GT, Gerecht K, Muir TW. Ubiquitin utilizes an acidic surface patch to alter chromatin structure. Nat Chem Biol. 2017;13(1):105–10.
Article
CAS
PubMed
Google Scholar
Kalashnikova AA, Porter-Goff ME, Muthurajan UM, Luger K, Hansen JC. The role of the nucleosome acidic patch in modulating higher order chromatin structure. J R Soc Interface. 2013;10(82):20121022.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dorigo B, Schalch T, Kulangara A, Duda S, Schroeder RR, Richmond TJ. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science. 2004;306(5701):1571–3.
Article
CAS
PubMed
Google Scholar
Chodaparambil JV, Barbera AJ, Lu X, Kaye KM, Hansen JC, Luger K. A charged and contoured surface on the nucleosome regulates chromatin compaction. Nat Struct Mol Biol. 2007;14(11):1105–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen Q, Yang R, Korolev N, Liu CF, Nordenskiold L. Regulation of Nucleosome stacking and chromatin compaction by the histone H4 N-Terminal Tail-H2A acidic patch interaction. J Mol Biol. 2017;429(13):2075–92.
Article
CAS
PubMed
Google Scholar
Sinha D, Shogren-Knaak MA. Role of direct interactions between the histone H4 Tail and the H2A core in long range nucleosome contacts. J Biol Chem. 2010;285(22):16572–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woodcock CL, Skoultchi AI, Fan Y. Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length. Chromosome Res. 2006;14(1):17–25.
Article
CAS
PubMed
Google Scholar
Lu X, Hansen JC. Identification of specific functional subdomains within the linker histone H10 C-terminal domain. J Biol Chem. 2004;279(10):8701–7.
Article
CAS
PubMed
Google Scholar
Carruthers LM, Hansen JC. The core histone N termini function independently of linker histones during chromatin condensation. J Biol Chem. 2000;275(47):37285–90.
Article
CAS
PubMed
Google Scholar
Mishra LN, Hayes JJ. A nucleosome-free region locally abrogates histone H1-dependent restriction of linker DNA accessibility in chromatin. J Biol Chem. 2018;293(50):19191–200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hansen JC, Connolly M, McDonald CJ, Pan A, Pryamkova A, Ray K, Seidel E, Tamura S, Rogge R, Maeshima K. The 10-nm chromatin fiber and its relationship to interphase chromosome organization. Biochem Soc Trans. 2018;46(1):67–76.
Article
CAS
PubMed
Google Scholar
Maeshima K, Matsuda T, Shindo Y, Imamura H, Tamura S, Imai R, Kawakami S, Nagashima R, Soga T, Noji H, et al. A transient rise in free Mg(2+) ions released from ATP-Mg hydrolysis contributes to mitotic chromosome condensation. Curr Biol. 2018;28(3):444–51.
Article
CAS
PubMed
Google Scholar
Lee JY, Hirose M. Partially folded state of the disulfide-reduced form of human serum albumin as an intermediate for reversible denaturation. J Biol Chem. 1992;267(21):14753–8.
Article
CAS
PubMed
Google Scholar
Muzzopappa F, Hertzog M, Erdel F. DNA length tunes the fluidity of DNA-based condensates. Biophys J. 2021;120(7):1288–300.
Article
CAS
PubMed
PubMed Central
Google Scholar
Correll SJ, Schubert MH, Grigoryev SA. Short nucleosome repeats impose rotational modulations on chromatin fibre folding. EMBO J. 2012;31(10):2416–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stanek D, Fox AH. Nuclear bodies: news insights into structure and function. Curr Opin Cell Biol. 2017;46:94–101.
Article
CAS
PubMed
Google Scholar
Aguzzi A, Altmeyer M. Phase separation: linking cellular compartmentalization to disease. Trends Cell Biol. 2016;26(7):547–58.
Article
CAS
PubMed
Google Scholar
Guo L, Shorter J. It’s raining liquids: RNA tunes viscoelasticity and dynamics of membraneless organelles. Mol Cell. 2015;60(2):189–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weber SC. Sequence-encoded material properties dictate the structure and function of nuclear bodies. Curr Opin Cell Biol. 2017;46:62–71.
Article
CAS
PubMed
Google Scholar
Zhou HX, Rivas G, Minton AP. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys. 2008;37:375–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turner AL, Watson M, Wilkins OG, Cato L, Travers A, Thomas JO, Stott K. Highly disordered histone H1-DNA model complexes and their condensates. Proc Natl Acad Sci USA. 2018;115(47):11964–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shakya A, Park S, Rana N, King JT. Liquid-liquid phase separation of histone proteins in cells: role in chromatin organization. Biophys J. 2020;118(3):753–64.
Article
CAS
PubMed
Google Scholar
Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1alpha suggests a role for phase separation in heterochromatin. Nature. 2017;547(7662):236–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH. Phase separation drives heterochromatin domain formation. Nature. 2017;547(7662):241–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Plys AJ, Davis CP, Kim J, Rizki G, Keenen MM, Marr SK, Kingston RE. Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2. Genes Dev. 2019;33(13–14):799–813.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tatavosian R, Kent S, Brown K, Yao T, Duc HN, Huynh TN, Zhen CY, Ma B, Wang H, Ren X. Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation. J Biol Chem. 2019;294(5):1451–63.
Article
CAS
PubMed
Google Scholar
Zhao S, Cheng L, Gao Y, Zhang B, Zheng X, Wang L, Li P, Sun Q, Li H. Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation. Cell Res. 2019;29(1):54–66.
Article
CAS
PubMed
Google Scholar
Fan C, Zhang H, Fu L, Li Y, Du Y, Qiu Z, Lu F. Rett mutations attenuate phase separation of MeCP2. Cell Discov. 2020;6(1):38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li CH, Coffey EL, Dall’Agnese A, Hannett NM, Tang X, Henninger JE, Platt JM, Oksuz O, Zamudio AV, Afeyan LK, et al. MeCP2 links heterochromatin condensates and neurodevelopmental disease. Nature. 2020;586(7829):440–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Hu M, Zuo MQ, Zhao J, Wu D, Huang L, Wen Y, Li Y, Chen P, Bao X, et al. Rett syndrome-causing mutations compromise MeCP2-mediated liquid-liquid phase separation of chromatin. Cell Res. 2020;30(5):393–407.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo Y, Zhao S, Wang GG. Polycomb gene silencing mechanisms: PRC2 chromatin targeting, H3K27me3 “Readout”, and phase separation-based compaction. Trends Genet. 2021;37(6):547–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Narlikar GJ. Phase-separation in chromatin organization. J Biosci. 2020;45(1):5.
Article
CAS
PubMed
Google Scholar
Kowalski A. Abundance of intrinsic structural disorder in the histone H1 subtypes. Comput Biol Chem. 2015;59 Pt A:16–27.
Article
PubMed
CAS
Google Scholar
Leicher R, Osunsade A, Latham AP, Chua GNL, Watters JW, Christodoulou-Rubalcava S, Zhang B, David Y, Liu S: Single-stranded nucleic acid sensing and coacervation by linker histone H1. bioRxiv 2021.
McSwiggen DT, Mir M, Darzacq X, Tjian R. Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes Dev. 2019;33(23–24):1619–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rego A, Sinclair PB, Tao W, Kireev I, Belmont AS. The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure. J Cell Sci. 2008;121(Pt 7):1119–27.
Article
CAS
PubMed
Google Scholar
Fussner E, Strauss M, Djuric U, Li R, Ahmed K, Hart M, Ellis J, Bazett-Jones DP. Open and closed domains in the mouse genome are configured as 10-nm chromatin fibres. Embo Rep. 2012;13(11):992–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature. 2001;410(6824):120–4.
Article
CAS
PubMed
Google Scholar
Jacobs SA, Taverna SD, Zhang Y, Briggs SD, Li J, Eissenberg JC, Allis CD, Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 2001;20(18):5232–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 2003;17(15):1870–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Erdel F, Rademacher A, Vlijm R, Tunnermann J, Frank L, Weinmann R, Schweigert E, Yserentant K, Hummert J, Bauer C, et al. Mouse heterochromatin adopts digital compaction states without showing hallmarks of HP1-driven liquid-liquid phase separation. Mol Cell. 2020;78(2):236–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, Jones RS, Zhang Y. Role of histone H2A ubiquitination in Polycomb silencing. Nature. 2004;431(7010):873–8.
Article
CAS
PubMed
Google Scholar
Saurin AJ, Shiels C, Williamson J, Satijn DP, Otte AP, Sheer D, Freemont PS. The human polycomb group complex associates with pericentromeric heterochromatin to form a novel nuclear domain. J Cell Biol. 1998;142(4):887–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ. HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature. 2019;575(7782):390–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Gao Y, Zheng X, Liu C, Dong S, Li R, Zhang G, Wei Y, Qu H, Li Y, et al. Histone modifications regulate chromatin compartmentalization by contributing to a phase separation mechanism. Mol Cell. 2019;76(4):646–59.
Article
CAS
PubMed
Google Scholar
Isono K, Endo Takaho A, Ku M, Yamada D, Suzuki R, Sharif J, Ishikura T, Toyoda T, Bernstein Bradley E, Koseki H. SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Dev Cell. 2013;26(6):565–77.
Article
CAS
PubMed
Google Scholar
Gao Z, Zhang J, Bonasio R, Strino F, Sawai A, Parisi F, Kluger Y, Reinberg D. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol Cell. 2012;45(3):344–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fang J, Chen T, Chadwick B, Li E, Zhang Y. Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J Biol Chem. 2004;279(51):52812–5.
Article
CAS
PubMed
Google Scholar
Cao R, Tsukada Y, Zhang Y. Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. Mol Cell. 2005;20(6):845–54.
Article
CAS
PubMed
Google Scholar
Seif E, Kang JJ, Sasseville C, Senkovich O, Kaltashov A, Boulier EL, Kapur I, Kim CA, Francis NJ. Phase separation by the polyhomeotic sterile alpha motif compartmentalizes Polycomb Group proteins and enhances their activity. Nat Commun. 2020;11(1):5609.
Article
CAS
PubMed
PubMed Central
Google Scholar
Adhireksan Z, Sharma D, Lee PL, Davey CA. Near-atomic resolution structures of interdigitated nucleosome fibres. Nat Commun. 2020;11(1):4747.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weidemann T, Wachsmuth M, Knoch TA, Muller G, Waldeck W, Langowski J. Counting nucleosomes in living cells with a combination of fluorescence correlation spectroscopy and confocal imaging. J Mol Biol. 2003;334(2):229–40.
Article
CAS
PubMed
Google Scholar
Hihara S, Pack CG, Kaizu K, Tani T, Hanafusa T, Nozaki T, Takemoto S, Yoshimi T, Yokota H, Imamoto N, et al. Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells. Cell Rep. 2012;2(6):1645–56.
Article
CAS
PubMed
Google Scholar
Strickfaden H, Missiaen K, Hendzel MJ, Underhill DA: KMT5C displays robust retention and liquid-like behavior in phase separated heterochromatin. bioRxiv 2019:776625.
Hendzel MJ, Kruhlak MJ, MacLean NA, Boisvert F, Lever MA, Bazett-Jones DP. Compartmentalization of regulatory proteins in the cell nucleus. J Steroid Biochem Mol Biol. 2001;76(1–5):9–21.
Article
CAS
PubMed
Google Scholar
Cho WK, Spille JH, Hecht M, Lee C, Li C, Grube V, Cisse II. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science. 2018;361(6400):412–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wiedner HJ, Giudice J. It’s not just a phase: function and characteristics of RNA-binding proteins in phase separation. Nat Struct Mol Biol. 2021;28(6):465–73.
Article
CAS
PubMed
Google Scholar
Miron E, Oldenkamp R, Brown JM, Pinto DMS, Xu CS, Faria AR, Shaban HA, Rhodes JDP, Innocent C, de Ornellas S, et al. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin. Sci Adv. 2020;6(39):eeba8811.
Article
CAS
Google Scholar
Hendzel MJ, Kruhlak MJ, Bazett-Jones DP. Organization of highly acetylated chromatin around sites of heterogeneous nuclear RNA accumulation. Mol Biol Cell. 1998;9(9):2491–507.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hilbert L, Sato Y, Kuznetsova K, Bianucci T, Kimura H, Julicher F, Honigmann A, Zaburdaev V, Vastenhouw NL. Transcription organizes euchromatin via microphase separation. Nat Commun. 2021;12(1):1360.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kwon I, Kato M, Xiang S, Wu L, Theodoropoulos P, Mirzaei H, Han T, Xie S, Corden JL, McKnight SL. Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains. Cell. 2013;155(5):1049–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu H, Yu D, Hansen AS, Ganguly S, Liu R, Heckert A, Darzacq X, Zhou Q. Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. Nature. 2018;558(7709):318–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Itoh Y, Iida S, Tamura S, Nagashima R, Shiraki K, Goto T, Hibino K, Ide S, Maeshima K. 1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells. Life Sci Alliance. 2021;4(4):e202001005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Narlikar GJ, Myong S, Larson D, Maeshima K, Francis N, Rippe K, Sabari B, Strader L, Tjian R. Is transcriptional regulation just going through a phase? Mol Cell. 2021;81(8):1579–85.
Article
CAS
PubMed
Google Scholar
Sabari BR, Dall’Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361(6400):eaar3958.
Article
PubMed
PubMed Central
CAS
Google Scholar
Guo YE, Manteiga JC, Henninger JE, Sabari BR, Dall’Agnese A, Hannett NM, Spille JH, Afeyan LK, Zamudio AV, Shrinivas K, et al. Pol II phosphorylation regulates a switch between transcriptional and splicing condensates. Nature. 2019;572(7770):543–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shin Y, Chang YC, Lee DSW, Berry J, Sanders DW, Ronceray P, Wingreen NS, Haataja M, Brangwynne CP. Liquid nuclear condensates mechanically sense and restructure the genome. Cell. 2018;175(6):1481–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zuo L, Zhang G, Massett M, Cheng J, Guo Z, Wang L, Gao Y, Li R, Huang X, Li P, et al. Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription. Nat Commun. 2021;12(1):1491.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fazio T, Visnapuu ML, Wind S, Greene EC. DNA curtains and nanoscale curtain rods: high-throughput tools for single molecule imaging. Langmuir. 2008;24(18):10524–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Frank L, Rippe K. Repetitive RNAs as regulators of chromatin-associated subcompartment formation by phase separation. J Mol Biol. 2020;432(15):4270–86.
Article
CAS
PubMed
Google Scholar
Mine-Hattab J, Heltberg M, Villemeur M, Guedj C, Mora T, Walczak AM, Dahan M, Taddei A. Single molecule microscopy reveals key physical features of repair foci in living cells. Elife. 2021;10:e60577.
Article
CAS
PubMed
PubMed Central
Google Scholar
Phair RD, Scaffidi P, Elbi C, Vecerova J, Dey A, Ozato K, Brown DT, Hager G, Bustin M, Misteli T. Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol. 2004;24(14):6393–402.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zinchenko A, Berezhnoy NV, Wang S, Rosencrans WM, Korolev N, van der Maarel JRC, Nordenskiold L. Single-molecule compaction of megabase-long chromatin molecules by multivalent cations. Nucleic Acids Res. 2018;46(2):635–49.
Article
CAS
PubMed
Google Scholar
Eltsov M, Maclellan KM, Maeshima K, Frangakis AS, Dubochet J. Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ. Proc Natl Acad Sci USA. 2008;105(50):19732–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Joti Y, Hikima T, Nishino Y, Kamada F, Hihara S, Takata H, Ishikawa T, Maeshima K. Chromosomes without a 30-nm chromatin fiber. Nucleus. 2012;3(5):404–10.
Article
PubMed
PubMed Central
Google Scholar
Nishino Y, Eltsov M, Joti Y, Ito K, Takata H, Takahashi Y, Hihara S, Frangakis AS, Imamoto N, Ishikawa T, et al. Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure. Embo J. 2012;31(7):1644–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Farr SE, Woods EJ, Joseph JA, Garaizar A, Collepardo-Guevara R. Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions. Nat Commun. 2021;12(1):2883.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chagin VO, Casas-Delucchi CS, Reinhart M, Schermelleh L, Markaki Y, Maiser A, Bolius JJ, Bensimon A, Fillies M, Domaing P, et al. 4D Visualization of replication foci in mammalian cells corresponding to individual replicons. Nat Commun. 2016;7:11231.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiang W, Roberti MJ, Hériché J-K, Huet S, Alexander S, Ellenberg J. Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. The dynamic structure of replication domains. J Cell Biol. 2018;217(6):1973–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ferreira J, Paolella G, Ramos C, Lamond AI. Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. J Cell Biol. 1997;139(7):1597–610.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olins DE, Olins AL. Epichromatin and chromomeres: a “fuzzy” perspective. Open Biol. 2018;8(6):180058.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nozaki T, Imai R, Tanbo M, Nagashima R, Tamura S, Tani T, Joti Y, Tomita M, Hibino K, Kanemaki MT, et al. Dynamic organization of chromatin domains revealed by super-resolution live-cell imaging. Mol Cell. 2017;67(2):282–93.
Article
CAS
PubMed
Google Scholar
Bintu B, Mateo LJ, Su JH, Sinnott-Armstrong NA, Parker M, Kinrot S, Yamaya K, Boettiger AN, Zhuang X. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science. 2018;362(6413):eaau1783.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M, Wang L, Milkie DE, Pasolli HA, Iyer N, Bogovic JA, et al. Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science. 2020;367(6475):eaaz5357.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berlum NL, Meisig J, Sedat JW, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485(7398):381–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G. Three-dimensional folding and functional organization principles of the drosophila genome. Cell. 2012;148(3):458–72.
Article
CAS
PubMed
Google Scholar
Dekker J, Heard E. Structural and functional diversity of topologically associating domains. FEBS Lett. 2015;589(20 Pt A):2877–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Su JH, Zheng P, Kinrot SS, Bintu B, Zhuang X. Genome-scale imaging of the 3D organization and transcriptional activity of chromatin. Cell. 2020;182(6):1641–59.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, et al. Cohesin Loss Eliminates All Loop Domains. Cell. 2017;171(2):305–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zuin J, Dixon JR, vander Reijden MI, Ye Z, Kolovos P, Brouwer RW, vande Corput MP, vande Werken HJ, Knoch TA, van Wilfred IF, et al. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci U S A. 2014;111(3):996–1001.
Article
CAS
PubMed
Google Scholar
Wutz G, Varnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, et al. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 2017;36(24):3573–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luppino JM, Park DS, Nguyen SC, Lan Y, Xu Z, Yunker R, Joyce EF. Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes. Nat Genet. 2020;52(8):840–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thiecke MJ, Wutz G, Muhar M, Tang W, Bevan S, Malysheva V, Stocsits R, Neumann T, Zuber J, Fraser P, et al. Cohesin-dependent and -independent mechanisms mediate chromosomal contacts between promoters and enhancers. Cell Rep. 2020;32(3):107929.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kimura H, Cook PR. Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J Cell Biol. 2001;153(7):1341–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lever MA, Th’ng JP, Sun X, Hendzel MJ. Rapid exchange of histone H1’1 on chromatin in living human cells. Nature. 2000;408(6814):873–6.
Article
CAS
PubMed
Google Scholar
Phair RD, Misteli T. High mobility of proteins in the mammalian cell nucleus. Nature. 2000;404(6778):604–9.
Article
CAS
PubMed
Google Scholar
Boskovic A, Eid A, Pontabry J, Ishiuchi T, Spiegelhalter C, Raghu Ram EV, Meshorer E, Torres-Padilla ME. Higher chromatin mobility supports totipotency and precedes pluripotency in vivo. Genes Dev. 2014;28(10):1042–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Strickfaden H, Zunhammer A, van Koningsbruggen S, Kohler D, Cremer T. 4D chromatin dynamics in cycling cells: Theodor Boveri’s hypotheses revisited. Nucleus. 2010;1(3):284–97.
PubMed
PubMed Central
Google Scholar
Bouck DC, Bloom K. Pericentric chromatin is an elastic component of the mitotic spindle. Curr Biol. 2007;17(9):741–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shimamoto Y, Tamura S, Masumoto H, Maeshima K. Nucleosome-nucleosome interactions via histone tails and linker DNA regulate nuclear rigidity. Mol Biol Cell. 2017;28(11):1580–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stephens AD, Banigan EJ, Adam SA, Goldman RD, Marko JF. Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Mol Biol Cell. 2017;28(14):1984–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wintner O, Hirsch-Attas N, Schlossberg M, Brofman F, Friedman R, Kupervaser M, Kitsberg D, Buxboim A. A unified linear viscoelastic model of the cell nucleus defines the mechanical contributions of lamins and chromatin. Adv Sci. 2020;7(8):1901222.
Article
CAS
Google Scholar
Schreiner SM, Koo PK, Zhao Y, Mochrie SG, King MC. The tethering of chromatin to the nuclear envelope supports nuclear mechanics. Nat Commun. 2015;6:7159.
Article
PubMed
Google Scholar
Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Ritland Politz JC, Tait LJ, et al. HP1alpha is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. Elife. 2021;10:e63972.
Article
PubMed
PubMed Central
Google Scholar
Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Politz JCR, Tait LJ et al. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. bioRxiv 2020.
Peters AH, O’Carroll D, Scherthan H, Mechtler K, Sauer S, Schofer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A, et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell. 2001;107(3):323–37.
Article
CAS
PubMed
Google Scholar
Canzio D, Chang EY, Shankar S, Kuchenbecker KM, Simon MD, Madhani HD, Narlikar GJ, Al-Sady B. Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly. Mol Cell. 2011;41(1):67–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nava MM, Miroshnikova YA, Biggs LC, Whitefield DB, Metge F, Boucas J, Vihinen H, Jokitalo E, Li X, Garcia Arcos JM, et al. Heterochromatin-driven nuclear softening protects the genome against mechanical stress-induced damage. Cell. 2020;181(4):800–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF. Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Mol Biol Cell. 2018;29(2):220–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O’Halloran T, Adam SA, Goldman RD, et al. Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation. Mol Biol Cell. 2019;30(17):2320–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ghosh S, Seelbinder B, Henderson JT, Watts RD, Scott AK, Veress AI, Neu CP. Deformation microscopy for dynamic intracellular and intranuclear mapping of mechanics with high spatiotemporal resolution. Cell Rep. 2019;27(5):1607–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinett CC, Straight A, Li G, Willhelm C, Sudlow G, Murray A, Belmont AS. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J Cell Biol. 1996;135(6 Pt 2):1685–700.
Article
CAS
PubMed
Google Scholar
Chubb JR, Boyle S, Perry P, Bickmore WA. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol. 2002;12(6):439–45.
Article
CAS
PubMed
Google Scholar
Hajjoul H, Mathon J, Ranchon H, Goiffon I, Mozziconacci J, Albert B, Carrivain P, Victor JM, Gadal O, Bystricky K, et al. High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome. Genome Res. 2013;23(11):1829–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heun P, Laroche T, Shimada K, Furrer P, Gasser SM. Chromosome dynamics in the yeast interphase nucleus. Science. 2001;294(5549):2181–6.
Article
CAS
PubMed
Google Scholar
Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol. 1997;7(12):930–9.
Article
CAS
PubMed
Google Scholar
Levi V, Ruan Q, Plutz M, Belmont AS, Gratton E. Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope. Biophys J. 2005;89(6):4275–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meister P, Towbin BD, Pike BL, Ponti A, Gasser SM. The spatial dynamics of tissue-specific promoters during C. elegans development. Genes Dev. 2010;24(8):766–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arai R, Sugawara T, Sato Y, Minakuchi Y, Toyoda A, Nabeshima K, Kimura H, Kimura A. Reduction in chromosome mobility accompanies nuclear organization during early embryogenesis in Caenorhabditis elegans. Sci Rep. 2017;7(1):3631.
Article
PubMed
PubMed Central
CAS
Google Scholar
Germier T, Kocanova S, Walther N, Bancaud A, Shaban HA, Sellou H, Politi AZ, Ellenberg J, Gallardo F, Bystricky K. Real-time imaging of a single gene reveals transcription-initiated local confinement. Biophys J. 2017;113(7):1383–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, et al. CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. Nucleic Acids Res. 2018;46(17):e100.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013;155(7):1479–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gu B, Swigut T, Spencley A, Bauer MR, Chung M, Meyer T, Wysocka J. Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements. Science. 2018;359(6379):1050–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma H, Tu LC, Chung YC, Naseri A, Grunwald D, Zhang S, Pederson T. Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. J Cell Biol. 2019;218(5):1467–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dundr M, Ospina JK, Sung MH, John S, Upender M, Ried T, Hager GL, Matera AG. Actin-dependent intranuclear repositioning of an active gene locus in vivo. J Cell Biol. 2007;179(6):1095–103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Khanna N, Hu Y, Belmont AS. HSP70 transgene directed motion to nuclear speckles facilitates heat shock activation. Curr Biol. 2014;24(10):1138–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang A, Kolhe JA, Gioacchini N, Baade I, Brieher WM, Peterson CL, Freeman BC. Mechanism of long-range chromosome motion triggered by gene activation. Dev Cell. 2020;52(3):309–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zidovska A, Weitz DA, Mitchison TJ. Micron-scale coherence in interphase chromatin dynamics. Proc Natl Acad Sci USA. 2013;110(39):15555–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shaban HA, Barth R, Bystricky K. Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription. Nucleic Acids Res. 2018;46(13):e77.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xiang W, Roberti MJ, Heriche JK, Huet S, Alexander S, Ellenberg J. Correction: correlative live and super-resolution imaging reveals the dynamic structure of replication domains. J Cell Biol. 2018;217(9):3315–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagashima R, Hibino K, Ashwin SS, Babokhov M, Fujishiro S, Imai R, Nozaki T, Tamura S, Tani T, Kimura H, et al. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J Cell Biol. 2019;218:1511–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shaban HA, Barth R, Bystricky K: Nanoscale mapping of DNA dynamics in live human cells. bioRxiv 2019.
Ashwin SS, Maeshima K, Sasai M. Heterogeneous fluid-like movements of chromatin and their implications to transcription. Biophys Rev. 2020;12(2):461–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ashwin SS, Nozaki T, Maeshima K, Sasai M. Organization of fast and slow chromatin revealed by single-nucleosome dynamics. Proc Natl Acad Sci U S A. 2019;116(40):19939–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Itoh Y, Woods EJ, Minami K, Maeshima K, Collepardo-Guevara R. Liquid-like chromatin in the cell: what can we learn from imaging and computational modeling? Curr Opin Struc Biol. 2021;71:123–35.
Article
CAS
Google Scholar
Espinosa JR, Joseph JA, Sanchez-Burgos I, Garaizar A, Frenkel D, Collepardo-Guevara R. Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components. Proc Natl Acad Sci U S A. 2020;117(24):13238–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Soutoglou E, Misteli T. Mobility and immobility of chromatin in transcription and genome stability. Curr Opin Genet Dev. 2007;17(5):435–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seeber A, Hauer MH, Gasser SM. chromosome dynamics in response to DNA damage. Annu Rev Genet. 2018;52:295–319.
Article
CAS
PubMed
Google Scholar
Hiragami-Hamada K, Soeroes S, Nikolov M, Wilkins B, Kreuz S, Chen C, De La Rosa-Velazquez IA, Zenn HM, Kost N, Pohl W, et al. Dynamic and flexible H3K9me3 bridging via HP1beta dimerization establishes a plastic state of condensed chromatin. Nat Commun. 2016;7:11310.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dion V, Kalck V, Seeber A, Schleker T, Gasser SM. Cohesin and the nucleolus constrain the mobility of spontaneous repair foci. Embo Rep. 2013;14(11):984–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Strickfaden H, Sharma AK, Hendzel MJ: A charge-dependent phase transition determines interphase chromatin organization. bioRxiv 2019:541086.
Lerner J, Gomez-Garcia PA, McCarthy RL, Liu Z, Lakadamyali M, Zaret KS. Two-parameter mobility assessments discriminate diverse regulatory factor behaviors in chromatin. Mol Cell. 2020;79(4):677–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Machida S, Takizawa Y, Ishimaru M, Sugita Y, Sekine S, Nakayama JI, Wolf M, Kurumizaka H. Structural basis of heterochromatin formation by human HP1. Mol Cell. 2018;69(3):385–97.
Article
CAS
PubMed
Google Scholar
Cremer T, Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol. 2010;2(3):a003889.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hebbes TR, Clayton AL, Thorne AW, Crane-Robinson C. Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken beta-globin chromosomal domain. EMBO J. 1994;13(8):1823–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gorisch SM, Wachsmuth M, Toth KF, Lichter P, Rippe K. Histone acetylation increases chromatin accessibility. J Cell Sci. 2005;118(Pt 24):5825–34.
Article
PubMed
CAS
Google Scholar
Ricci MA, Manzo C, Garcia-Parajo MF, Lakadamyali M, Cosma MP. Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell. 2015;160(6):1145–58.
Article
CAS
PubMed
Google Scholar
Amitai A, Seeber A, Gasser SM, Holcman D. Visualization of chromatin decompaction and break site extrusion as predicted by statistical polymer modeling of single-locus trajectories. Cell Rep. 2017;18(5):1200–14.
Article
CAS
PubMed
Google Scholar
Albiez H, Cremer M, Tiberi C, Vecchio L, Schermelleh L, Dittrich S, Kupper K, Joffe B, Thormeyer T, von Hase J, et al. Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosome Res. 2006;14(7):707–33.
Article
CAS
PubMed
Google Scholar
Nasmyth K, Haering CH. The structure and function of SMC and kleisin complexes. Annu Rev Biochem. 2005;74:595–648.
Article
CAS
PubMed
Google Scholar
Morales C, Losada A. Establishing and dissolving cohesion during the vertebrate cell cycle. Curr Opin Cell Biol. 2018;52:51–7.
Article
CAS
PubMed
Google Scholar
Nishiyama T. Cohesion and cohesin-dependent chromatin organization. Curr Opin Cell Biol. 2019;58:8–14.
Article
CAS
PubMed
Google Scholar
Chen H, Levo M, Barinov L, Fujioka M, Jaynes JB, Gregor T. Dynamic interplay between enhancer-promoter topology and gene activity. Nat Genet. 2018;50(9):1296–303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shaban HA, Barth R, Recoules L, Bystricky K. Hi-D: nanoscale mapping of nuclear dynamics in single living cells. Genome Biol. 2020;21(1):95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM, Cattoglio C, Heckert A, Banala S, Lavis L, Darzacq X, et al. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science. 2018;361(6400):eaar2555.
Article
PubMed
PubMed Central
CAS
Google Scholar
Feuerborn A, Cook PR. Why the activity of a gene depends on its neighbors. Trends Genet. 2015;31(9):483–90.
Article
CAS
PubMed
Google Scholar
Edelman LB, Fraser P. Transcription factories: genetic programming in three dimensions. Curr Opin Genet Dev. 2012;22(2):110–4.
Article
CAS
PubMed
Google Scholar
Ide T, Ochi H, Imai R, Maeshima K. Transcriptional suppression of ribosomal DNA with phase separation. Sci Adv. 2020;6(42):eabb5953.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shinkai S, Nozaki T, Maeshima K, Togashi Y. Dynamic nucleosome movement tells structural information of topological chromatin domains in human cells. PLoS Computa Biol. 2016;12(10):e1005136.
Article
CAS
Google Scholar
van Steensel B, Belmont AS. Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell. 2017;169(5):780–91.
Article
PubMed
PubMed Central
CAS
Google Scholar
Edgeworth R, Dalton BJ, Parnell T. The pitch drop experiment. Eur J Phys. 1984;5(4):198–200.
Article
Google Scholar
Erdel F. Biophysical mechanisms of chromatin patterning. Curr Opin Genet Dev. 2020;61:62–8.
Article
CAS
PubMed
Google Scholar
Zidovska A. Chromatin: liquid or solid? Cell. 2020;183(7):1737–9.
Article
CAS
PubMed
Google Scholar
Vivante A, Bronshtein I, Garini Y. Chromatin viscoelasticity measured by local dynamic analysis. Biophys J. 2020;118(9):2258–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet. 2001;2(4):292–301.
Article
CAS
PubMed
Google Scholar
Maeshima K, Tamura S, Hansen JC, Itoh Y. Fluid-like chromatin: toward understanding the real chromatin organization present in the cell. Curr Opin Cell Biol. 2020;64:77–89.
Article
CAS
PubMed
Google Scholar