1932

Abstract

In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome–nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. In this review, we provide a summary of recent progress on the structure of chromatin fibers in vitro and in the nucleus, highlight studies on the dynamic regulation of chromatin fibers, and discuss their related biological functions and abnormal organization in diseases.

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2021-05-06
2024-10-12
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Literature Cited

  1. 1. 
    Alexandrow MG, Hamlin JL. 2005. Chromatin decondensation in S-phase involves recruitment of Cdk2 by Cdc45 and histone H1 phosphorylation. J. Cell Biol. 168:875–86
    [Google Scholar]
  2. 2. 
    Allan J, Hartman PG, Crane-Robinson C, Aviles FX. 1980. The structure of histone H1 and its location in chromatin. Nature 288:675–79
    [Google Scholar]
  3. 3. 
    Allshire RC, Karpen GH. 2008. Epigenetic regulation of centromeric chromatin: old dogs, new tricks?. Nat. Rev. Genet. 9:923–37
    [Google Scholar]
  4. 4. 
    Arents G, Moudrianakis EN. 1993. Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. PNAS 90:10489–93
    [Google Scholar]
  5. 5. 
    Bassett EA, DeNizio J, Barnhart-Dailey MC, Panchenko T, Sekulic N et al. 2012. HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly. Dev. Cell 22:749–62
    [Google Scholar]
  6. 6. 
    Bednar J, Garcia-Saez I, Boopathi R, Cutter AR, Papai G et al. 2017. Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1. Mol. Cell 66:384–97.e8
    [Google Scholar]
  7. 7. 
    Bednar J, Horowitz RA, Grigoryev SA, Carruthers LM, Hansen JC et al. 1998. Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. PNAS 95:14173–78
    [Google Scholar]
  8. 8. 
    Belotserkovskaya R, Oh S, Bondarenko VA, Orphanides G, Studitsky VM, Reinberg D. 2003. FACT facilitates transcription-dependent nucleosome alteration. Science 301:1090–93
    [Google Scholar]
  9. 9. 
    Bennett RL, Bele A, Small EC, Will CM, Nabet B et al. 2019. A mutation in histone H2B represents a new class of oncogenic driver. Cancer Discov 9:1438–51
    [Google Scholar]
  10. 10. 
    Black BE, Foltz DR, Chakravarthy S, Luger K, Woods VL Jr., Cleveland DW. 2004. Structural determinants for generating centromeric chromatin. Nature 430:578–82
    [Google Scholar]
  11. 11. 
    Cato L, Stott K, Watson M, Thomas JO. 2008. The interaction of HMGB1 and linker histones occurs through their acidic and basic tails. J. Mol. Biol. 384:1262–72
    [Google Scholar]
  12. 12. 
    Chahrour M, Zoghbi HY. 2007. The story of Rett syndrome: from clinic to neurobiology. Neuron 56:422–37
    [Google Scholar]
  13. 13. 
    Chen P, Wang Y, Li G. 2014. Dynamics of histone variant H3.3 and its coregulation with H2A.Z at enhancers and promoters. Nucleus 5:21–27
    [Google Scholar]
  14. 14. 
    Chen P, Zhao J, Wang Y, Wang M, Long H et al. 2013. H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev 27:2109–24
    [Google Scholar]
  15. 15. 
    Chen Y, Tokuda JM, Topping T, Meisburger SP, Pabit SA et al. 2017. Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. PNAS 114:334–39
    [Google Scholar]
  16. 16. 
    Cirillo LA, Lin FR, Cuesta I, Friedman D, Jarnik M, Zaret KS. 2002. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell 9:279–89
    [Google Scholar]
  17. 17. 
    Clark KL, Halay ED, Lai E, Burley SK. 1993. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature 364:412–20
    [Google Scholar]
  18. 18. 
    Collepardo-Guevara R, Schlick T. 2014. Chromatin fiber polymorphism triggered by variations of DNA linker lengths. PNAS 111:8061–66
    [Google Scholar]
  19. 19. 
    Correll SJ, Schubert MH, Grigoryev SA. 2012. Short nucleosome repeats impose rotational modulations on chromatin fibre folding. EMBO J 31:2416–26
    [Google Scholar]
  20. 20. 
    Dalal Y, Wang H, Lindsay S, Henikoff S. 2007. Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLOS Biol 5:1798–809
    [Google Scholar]
  21. 21. 
    Daujat S, Zeissler U, Waldmann T, Happel N, Schneider R. 2005. HP1 binds specifically to Lys26-methylated histone H1.4, whereas simultaneous Ser27 phosphorylation blocks HP1 binding. J. Biol. Chem. 280:38090–95
    [Google Scholar]
  22. 22. 
    Dekker J, Rippe K, Dekker M, Kleckner N. 2002. Capturing chromosome conformation. Science 295:1306–11
    [Google Scholar]
  23. 23. 
    Della Ragione F, Vacca M, Fioriniello S, Pepe G, D'Esposito M 2016. MECP2, a multi-talented modulator of chromatin architecture. Brief Funct. Genom. 15:420–31
    [Google Scholar]
  24. 24. 
    Depken M, Schiessel H. 2009. Nucleosome shape dictates chromatin fiber structure. Biophys. J. 96:777–84
    [Google Scholar]
  25. 25. 
    Dodd IB, Micheelsen MA, Sneppen K, Thon G. 2007. Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129:813–22
    [Google Scholar]
  26. 26. 
    Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P. 2020. Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature 580:669–72
    [Google Scholar]
  27. 27. 
    Dorigo B, Schalch T, Kulangara A, Duda S, Schroeder RR, Richmond TJ. 2004. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306:1571–73
    [Google Scholar]
  28. 28. 
    Doyen CM, Montel F, Gautier T, Menoni H, Claudet C et al. 2006. Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome. EMBO J 25:4234–44
    [Google Scholar]
  29. 29. 
    Drane P, Ouararhni K, Depaux A, Shuaib M, Hamiche A. 2010. The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev 24:1253–65
    [Google Scholar]
  30. 30. 
    Dunleavy EM, Roche D, Tagami H, Lacoste N, Ray-Gallet D et al. 2009. HJURP is a cell-cycle-dependent maintenance and deposition factor of CENP-A at centromeres. Cell 137:485–97
    [Google Scholar]
  31. 31. 
    Ekundayo B, Richmond TJ, Schalch T. 2017. Capturing structural heterogeneity in chromatin fibers. J. Mol. Biol. 429:3031–42
    [Google Scholar]
  32. 32. 
    Escobar TM, Oksuz O, Saldana-Meyer R, Descostes N, Bonasio R, Reinberg D. 2019. Active and repressed chromatin domains exhibit distinct nucleosome segregation during DNA replication. Cell 179:953–63.e11
    [Google Scholar]
  33. 33. 
    Falk SJ, Guo LY, Sekulic N, Smoak EM, Mani T et al. 2015. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Science 348:699–703
    [Google Scholar]
  34. 34. 
    Fan JY, Rangasamy D, Luger K, Tremethick DJ. 2004. H2A.Z alters the nucleosome surface to promote HP1α-mediated chromatin fiber folding. Mol. Cell 16:655–61
    [Google Scholar]
  35. 35. 
    Fan Y, Nikitina T, Zhao J, Fleury TJ, Bhattacharyya R et al. 2005. Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell 123:1199–212
    [Google Scholar]
  36. 36. 
    Fang J, Liu Y, Wei Y, Deng W, Yu Z et al. 2015. Structural transitions of centromeric chromatin regulate the cell cycle-dependent recruitment of CENP-N. Genes Dev 29:1058–73
    [Google Scholar]
  37. 37. 
    Fang Q, Chen P, Wang M, Fang J, Yang N et al. 2016. Human cytomegalovirus IE1 protein alters the higher-order chromatin structure by targeting the acidic patch of the nucleosome. eLife 5:e11911
    [Google Scholar]
  38. 38. 
    Flex E, Martinelli S, Van Dijck A, Ciolfi A, Cecchetti S et al. 2019. Aberrant function of the C-terminal tail of HIST1H1E accelerates cellular senescence and causes premature aging. Am. J. Hum. Genet. 105:493–508
    [Google Scholar]
  39. 39. 
    Foltz DR, Jansen LE, Bailey AO, Yates JR 3rd, Bassett EA et al. 2009. Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell 137:472–84
    [Google Scholar]
  40. 40. 
    Fujimoto M, Takaki E, Takii R, Tan K, Prakasam R et al. 2012. RPA assists HSF1 access to nucleosomal DNA by recruiting histone chaperone FACT. Mol. Cell 48:182–94
    [Google Scholar]
  41. 41. 
    Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H et al. 2009. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58–64
    [Google Scholar]
  42. 42. 
    Fussner E, Djuric U, Strauss M, Hotta A, Perez-Iratxeta C et al. 2011. Constitutive heterochromatin reorganization during somatic cell reprogramming. EMBO J 30:1778–89
    [Google Scholar]
  43. 43. 
    Gan L, Ladinsky MS, Jensen GJ. 2013. Chromatin in a marine picoeukaryote is a disordered assemblage of nucleosomes. Chromosoma 122:377–86
    [Google Scholar]
  44. 44. 
    Garcia-Saez I, Menoni H, Boopathi R, Shukla MS, Soueidan L et al. 2018. Structure of an H1-bound 6-nucleosome array reveals an untwisted two-start chromatin fiber conformation. Mol. Cell 72:902–15.e7
    [Google Scholar]
  45. 45. 
    Ghosh RP, Horowitz-Scherer RA, Nikitina T, Shlyakhtenko LS, Woodcock CL. 2010. MeCP2 binds cooperatively to its substrate and competes with histone H1 for chromatin binding sites. Mol. Cell. Biol. 30:4656–70
    [Google Scholar]
  46. 46. 
    Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ et al. 2010. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140:678–91
    [Google Scholar]
  47. 47. 
    Gonzalez-Rincon J, Mendez M, Gomez S, Garcia JF, Martin P et al. 2019. Unraveling transformation of follicular lymphoma to diffuse large B-cell lymphoma. PLOS ONE 14:e0212813
    [Google Scholar]
  48. 48. 
    Grigoryev SA, Bascom G, Buckwalter JM, Schubert MB, Woodcock CL, Schlick T. 2016. Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes. PNAS 113:1238–43
    [Google Scholar]
  49. 49. 
    Hendzel MJ, Lever MA, Crawford E, Th'ng JP 2004. The C-terminal domain is the primary determinant of histone H1 binding to chromatin in vivo. J. Biol. Chem. 279:20028–34
    [Google Scholar]
  50. 50. 
    Hondele M, Stuwe T, Hassler M, Halbach F, Bowman A et al. 2013. Structural basis of histone H2A-H2B recognition by the essential chaperone FACT. Nature 499:111–14
    [Google Scholar]
  51. 51. 
    Horowitz RA, Agard DA, Sedat JW, Woodcock CL. 1994. The three-dimensional architecture of chromatin in situ: Electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon. J. Cell Biol. 125:1–10
    [Google Scholar]
  52. 52. 
    Hsieh TH, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. 2015. Mapping nucleosome resolution chromosome folding in yeast by micro-C. Cell 162:108–19
    [Google Scholar]
  53. 53. 
    Hsieh TS, Cattoglio C, Slobodyanyuk E, Hansen AS, Rando OJ et al. 2020. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Mol. Cell 78:539–53.e8
    [Google Scholar]
  54. 54. 
    Hu H, Liu Y, Wang M, Fang J, Huang H et al. 2011. Structure of a CENP-A-histone H4 heterodimer in complex with chaperone HJURP. Genes Dev 25:901–6
    [Google Scholar]
  55. 55. 
    Izzo A, Kamieniarz K, Schneider R. 2008. The histone H1 family: specific members, specific functions?. Biol. Chem. 389:333–43
    [Google Scholar]
  56. 56. 
    Jiang D, Berger F. 2017. DNA replication-coupled histone modification maintains Polycomb gene silencing in plants. Science 357:1146–49
    [Google Scholar]
  57. 57. 
    Kamieniarz K, Izzo A, Dundr M, Tropberger P, Ozretic L et al. 2012. A dual role of linker histone H1.4 Lys 34 acetylation in transcriptional activation. Genes Dev 26:797–802
    [Google Scholar]
  58. 58. 
    Kasinsky HE, Lewis JD, Dacks JB, Ausio J. 2001. Origin of H1 linker histones. FASEB J 15:34–42
    [Google Scholar]
  59. 59. 
    Kassabov SR, Zhang B, Persinger J, Bartholomew B. 2003. SWI/SNF unwraps, slides, and rewraps the nucleosome. Mol. Cell 11:391–403
    [Google Scholar]
  60. 60. 
    Kato H, Jiang J, Zhou BR, Rozendaal M, Feng H et al. 2013. A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Science 340:1110–13
    [Google Scholar]
  61. 61. 
    Kato H, van Ingen H, Zhou BR, Feng H, Bustin M et al. 2011. Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. PNAS 108:12283–88
    [Google Scholar]
  62. 62. 
    Kaufman PD, Rando OJ. 2010. Chromatin as a potential carrier of heritable information. Curr. Opin. Cell Biol. 22:284–90
    [Google Scholar]
  63. 63. 
    Kiteyski-LeBlanc JL, Yuwen T, Dyer PN, Rudolph J, Luger K, Kay LE. 2018. Investigating the dynamics of destabilized nucleosomes using methyl-TROSY NMR. J. Am. Chem. Soc. 140:4774–77
    [Google Scholar]
  64. 64. 
    Koopmans WJ, Brehm A, Logie C, Schmidt T, van Noort J. 2007. Single-pair FRET microscopy reveals mononucleosome dynamics. J. Fluoresc. 17:785–95
    [Google Scholar]
  65. 65. 
    Koslover EF, Fuller C, Straight AF, Spakowitz AJ. 2010. Role of DNA elasticity and nucleosome geometry in hierarchical packaging of chromatin. Biophys. J. 98:474a
    [Google Scholar]
  66. 66. 
    Krietenstein N, Rando OJ. 2020. Mesoscale organization of the chromatin fiber. Curr. Opin. Genet. Dev. 61:32–36
    [Google Scholar]
  67. 67. 
    Krishnakumar R, Kraus WL. 2010. PARP-1 regulates chromatin structure and transcription through a KDM5B-dependent pathway. Mol. Cell 39:736–49
    [Google Scholar]
  68. 68. 
    Li G, Margueron R, Hu G, Stokes D, Wang YH, Reinberg D. 2010. Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo. Mol. Cell 38:41–53
    [Google Scholar]
  69. 69. 
    Li W, Chen P, Yu J, Dong L, Liang D et al. 2016. FACT remodels the tetranucleosomal unit of chromatin fibers for gene transcription. Mol. Cell 64:120–33
    [Google Scholar]
  70. 70. 
    Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–93
    [Google Scholar]
  71. 71. 
    Lu X, Hansen JC. 2004. Identification of specific functional subdomains within the linker histone H10 C-terminal domain. J. Biol. Chem. 279:8701–7
    [Google Scholar]
  72. 72. 
    Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–60
    [Google Scholar]
  73. 73. 
    Lyst MJ, Ekiert R, Ebert DH, Merusi C, Nowak J et al. 2013. Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor. Nat. Neurosci. 16:898–902
    [Google Scholar]
  74. 74. 
    Ma W, Gu C, Ma L, Fan C, Zhang C et al. 2020. Mixed secondary chromatin structure revealed by modeling radiation-induced DNA fragment length distribution. Sci. China Life Sci. 63:825–34
    [Google Scholar]
  75. 75. 
    Makarov VL, Dimitrov SI, Tsaneva IR, Pashev IG. 1984. The role of histone-H1 and non-structured domains of core histones in maintaining the orientation of nucleosomes within the chromatin fiber. Biochem. Biophys. Res. Commun. 122:1021–27
    [Google Scholar]
  76. 76. 
    Makde RD, England JR, Yennawar HP, Tan S. 2010. Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 467:562–66
    [Google Scholar]
  77. 77. 
    Manohar M, Mooney AM, North JA, Nakkula RJ, Picking JW et al. 2009. Acetylation of histone H3 at the nucleosome dyad alters DNA-histone binding. J. Biol. Chem. 284:23312–21
    [Google Scholar]
  78. 78. 
    Mareschal S, Pham-Ledard A, Viailly PJ, Dubois S, Bertrand P et al. 2017. Identification of somatic mutations in primary cutaneous diffuse large B-cell lymphoma, leg type by massive parallel sequencing. J. Investig. Dermatol. 137:1984–94
    [Google Scholar]
  79. 79. 
    Margueron R, Justin N, Ohno K, Sharpe ML, Son J et al. 2009. Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461:762–67
    [Google Scholar]
  80. 80. 
    Margueron R, Reinberg D. 2010. Chromatin structure and the inheritance of epigenetic information. Nat. Rev. Genet. 11:285–96
    [Google Scholar]
  81. 81. 
    McGhee JD, Nickol JM, Felsenfeld G, Rau DC. 1983. Higher order structure of chromatin: Orientation of nucleosomes within the 30 nm chromatin solenoid is independent of species and spacer length. Cell 33:831–41
    [Google Scholar]
  82. 82. 
    McGinty RK, Henrici RC, Tan S. 2014. Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature 514:591–96
    [Google Scholar]
  83. 83. 
    McGinty RK, Tan S. 2016. Recognition of the nucleosome by chromatin factors and enzymes. Curr. Opin. Struct. Biol. 37:54–61
    [Google Scholar]
  84. 84. 
    Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z et al. 2020. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science 368:1460–65
    [Google Scholar]
  85. 85. 
    Mihardja S, Spakowitz AJ, Zhang Y, Bustamante C. 2006. Effect of force on mononucleosomal dynamics. PNAS 103:15871–76
    [Google Scholar]
  86. 86. 
    Mivelaz M, Cao AM, Kubik S, Zencir S, Hovius R et al. 2020. Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor. Mol. Cell 77:488–500.e9
    [Google Scholar]
  87. 87. 
    Nacev BA, Feng L, Bagert JD, Lemiesz AE, Gao J et al. 2019. The expanding landscape of “oncohistone” mutations in human cancers. Nature 567:473–78
    [Google Scholar]
  88. 88. 
    Nan X, Campoy FJ, Bird A. 1997. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell 88:471–81
    [Google Scholar]
  89. 89. 
    Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM et al. 1998. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386–89
    [Google Scholar]
  90. 90. 
    Ngo TTM, Ha T. 2015. Nucleosomes undergo slow spontaneous gaping. Nucleic Acids Res 43:3964–71
    [Google Scholar]
  91. 91. 
    Ngo TTM, Zhang Q, Zhou R, Yodh JG, Ha T. 2015. Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility. Cell 160:1135–44
    [Google Scholar]
  92. 92. 
    Nikitina T, Ghosh RP, Horowitz-Scherer RA, Hansen JC, Grigoryev SA, Woodcock CL. 2007. MeCP2-chromatin interactions include the formation of chromatosome-like structures and are altered in mutations causing Rett syndrome. J. Biol. Chem. 282:28237–45
    [Google Scholar]
  93. 93. 
    Nishino Y, Eltsov M, Joti Y, Ito K, Takata H et al. 2012. Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure. EMBO J 31:1644–53
    [Google Scholar]
  94. 94. 
    Ohno M, Ando T, Priest DG, Kumar V, Yoshida Y, Taniguchi Y. 2019. Sub-nucleosomal genome structure reveals distinct nucleosome folding motifs. Cell 176:520–34.e25
    [Google Scholar]
  95. 95. 
    Oluwadare O, Highsmith M, Cheng J. 2019. An overview of methods for reconstructing 3-D chromosome and genome structures from Hi-C data. Biol. Proced. Online 21:7
    [Google Scholar]
  96. 96. 
    Ordu O, Kremser L, Lusser A, Dekker NH. 2018. Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics. J. Chem. Phys. 148:123323
    [Google Scholar]
  97. 97. 
    Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC 2017. ChromEMT: visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 357:eaag0025
    [Google Scholar]
  98. 98. 
    Polach KJ, Widom J. 1995. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254:130–49
    [Google Scholar]
  99. 99. 
    Postnikov Y, Bustin M. 2010. Regulation of chromatin structure and function by HMGN proteins. Biochim. Biophys. Acta 1799:62–68
    [Google Scholar]
  100. 100. 
    Postnikov YV, Bustin M. 2016. Functional interplay between histone H1 and HMG proteins in chromatin. Biochim. Biophys. Acta 1859:462–67
    [Google Scholar]
  101. 101. 
    Reinberg D, Vales LD. 2018. Chromatin domains rich in inheritance. Science 361:33–34
    [Google Scholar]
  102. 102. 
    Ricci MA, Manzo C, Garcia-Parajo MF, Lakadamyali M, Cosma MP. 2015. Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 160:1145–58
    [Google Scholar]
  103. 103. 
    Risca VI, Denny SK, Straight AF, Greenleaf WJ. 2017. Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping. Nature 541:237–41
    [Google Scholar]
  104. 104. 
    Robinson PJ, Fairall L, Huynh VA, Rhodes D. 2006. EM measurements define the dimensions of the “30-nm” chromatin fiber: evidence for a compact, interdigitated structure. PNAS 103:6506–11
    [Google Scholar]
  105. 105. 
    Rochman M, Malicet C, Bustin M. 2010. HMGN5/NSBP1: a new member of the HMGN protein family that affects chromatin structure and function. Biochim. Biophys. Acta 1799:86–92
    [Google Scholar]
  106. 106. 
    Rochman M, Postnikov Y, Correll S, Malicet C, Wincovitch S et al. 2009. The interaction of NSBP1/HMGN5 with nucleosomes in euchromatin counteracts linker histone-mediated chromatin compaction and modulates transcription. Mol. Cell 35:642–56
    [Google Scholar]
  107. 107. 
    Roque A, Ponte I, Suau P. 2016. Interplay between histone H1 structure and function. Biochim. Biophys. Acta 1859:444–54
    [Google Scholar]
  108. 108. 
    Roque A, Ponte I, Suau P. 2017. Post-translational modifications of the intrinsically disordered terminal domains of histone H1: effects on secondary structure and chromatin dynamics. Chromosoma 126:83–91
    [Google Scholar]
  109. 109. 
    Roulland Y, Ouararhni K, Naidenov M, Ramos L, Shuaib M et al. 2016. The flexible ends of CENP-A nucleosome are required for mitotic fidelity. Mol. Cell 63:674–85
    [Google Scholar]
  110. 110. 
    Routh A, Sandin S, Rhodes D. 2008. Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. PNAS 105:8872–77
    [Google Scholar]
  111. 111. 
    Rydberg B, Holley WR, Mian IS, Chatterjee A. 1998. Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fiber. J. Mol. Biol. 284:71–84
    [Google Scholar]
  112. 112. 
    Satchwell SC, Travers AA. 1989. Asymmetry and polarity of nucleosomes in chicken erythrocyte chromatin. EMBO J 8:229–38
    [Google Scholar]
  113. 113. 
    Schalch T, Duda S, Sargent DF, Richmond TJ. 2005. X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436:138–41
    [Google Scholar]
  114. 114. 
    Scheffer MP, Eltsov M, Frangakis AS. 2011. Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei. PNAS 108:16992–97
    [Google Scholar]
  115. 115. 
    Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E et al. 2012. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 482:226–31
    [Google Scholar]
  116. 116. 
    Shen H, Laird PW. 2013. Interplay between the cancer genome and epigenome. Cell 153:38–55
    [Google Scholar]
  117. 117. 
    Shimada M, Chen WY, Nakadai T, Onikubo T, Guermah M et al. 2019. Gene-specific H1 eviction through a transcriptional activator→p300→NAP1→H1 pathway. Mol. Cell 74:268–83.e5
    [Google Scholar]
  118. 118. 
    Shin HJ, Kim YE, Kim ET, Ahn JH. 2012. The chromatin-tethering domain of human cytomegalovirus immediate-early (IE) 1 mediates associations of IE1, PML and STAT2 with mitotic chromosomes, but is not essential for viral replication. J. Gen. Virol. 93:716–21
    [Google Scholar]
  119. 119. 
    Skene PJ, Illingworth RS, Webb S, Kerr AR, James KD et al. 2010. Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Mol. Cell 37:457–68
    [Google Scholar]
  120. 120. 
    Song F, Chen P, Sun D, Wang M, Dong L et al. 2014. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science 344:376–80
    [Google Scholar]
  121. 121. 
    Staynov DZ, Dunn S, Baldwin JP, Crane-Robinson C. 1983. Nuclease digestion patterns as a criterion for nucleosome orientation in the higher order structure of chromatin. FEBS Lett. 157:311–15
    [Google Scholar]
  122. 122. 
    Suto RK, Clarkson MJ, Tremethick DJ, Luger K. 2000. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat. Struct. Biol. 7:1121–24
    [Google Scholar]
  123. 123. 
    Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y et al. 2011. Crystal structure of the human centromeric nucleosome containing CENP-A. Nature 476:232–35
    [Google Scholar]
  124. 124. 
    Talbert PB, Henikoff S. 2006. Spreading of silent chromatin: inaction at a distance. Nat. Rev. Genet. 7:793–803
    [Google Scholar]
  125. 125. 
    Thoma F, Koller T, Klug A. 1979. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J. Cell Biol. 83:403–27
    [Google Scholar]
  126. 126. 
    Tosi A, Haas C, Herzog F, Gilmozzi A, Berninghausen O et al. 2013. Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell 154:1207–19
    [Google Scholar]
  127. 127. 
    Trojer P, Li G, Sims RJ 3rd, Vaquero A, Kalakonda N et al. 2007. L3MBTL1, a histone-methylation-dependent chromatin lock. Cell 129:915–28
    [Google Scholar]
  128. 128. 
    Vicent GP, Nacht AS, Font-Mateu J, Castellano G, Gaveglia L et al. 2011. Four enzymes cooperate to displace histone H1 during the first minute of hormonal gene activation. Genes Dev 25:845–62
    [Google Scholar]
  129. 129. 
    Vlijm R, Lee M, Lipfert J, Lusser A, Dekker C, Dekker NH. 2015. Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes. Cell Rep 10:216–25
    [Google Scholar]
  130. 130. 
    Wang L, Hu M, Zuo MQ, Zhao J, Wu D et al. 2020. Rett syndrome-causing mutations compromise MeCP2-mediated liquid-liquid phase separation of chromatin. Cell Res 30:393–407
    [Google Scholar]
  131. 131. 
    Wang Y, Long H, Yu J, Dong L, Wassef M et al. 2018. Histone variants H2A.Z and H3.3 coordinately regulate PRC2-dependent H3K27me3 deposition and gene expression regulation in mES cells. BMC Biol 16:107
    [Google Scholar]
  132. 132. 
    Wisniewski JR, Zougman A, Kruger S, Mann M. 2007. Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue. Mol. Cell Proteom. 6:72–87
    [Google Scholar]
  133. 133. 
    Wong H, Victor JM, Mozziconacci J. 2007. An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length. PLOS ONE 2:e877
    [Google Scholar]
  134. 134. 
    Woodcock CL, Frado LL, Rattner JB. 1984. The higher-order structure of chromatin: evidence for a helical ribbon arrangement. J. Cell Biol. 99:42–52
    [Google Scholar]
  135. 135. 
    Woodcock CL, Ghosh RP. 2010. Chromatin higher-order structure and dynamics. Cold Spring Harb. Perspect. Biol. 2:a000596
    [Google Scholar]
  136. 136. 
    Yang C, van der Woerd MJ, Muthurajan UM, Hansen JC, Luger K. 2011. Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes. Nucleic Acids Res 39:4122–35
    [Google Scholar]
  137. 137. 
    Yu Z, Zhou X, Wang W, Deng W, Fang J et al. 2015. Dynamic phosphorylation of CENP-A at Ser68 orchestrates its cell-cycle-dependent deposition at centromeres. Dev. Cell 32:68–81
    [Google Scholar]
  138. 138. 
    Yuan W, Wu T, Fu H, Dai C, Wu H et al. 2012. Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science 337:971–75
    [Google Scholar]
  139. 139. 
    Zhang Q, Giebler HA, Isaacson MK, Nyborg JK. 2015. Eviction of linker histone H1 by NAP-family histone chaperones enhances activated transcription. Epigenet. Chromatin 8:30
    [Google Scholar]
  140. 140. 
    Zhao J, Wang M, Chang L, Yu J, Song A et al. 2020. RYBP/YAF2-PRC1 complexes and histone H1-dependent chromatin compaction mediate propagation of H2AK119ub1 during cell division. Nat. Cell Biol. 22:439–52
    [Google Scholar]
  141. 141. 
    Zhao S, Bellone S, Lopez S, Thakral D, Schwab C et al. 2016. Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial-mesenchymal transition. PNAS 113:12238–43
    [Google Scholar]
  142. 142. 
    Zhou BR, Feng H, Kato H, Dai L, Yang Y et al. 2013. Structural insights into the histone H1-nucleosome complex. PNAS 110:19390–95
    [Google Scholar]
  143. 143. 
    Zhou BR, Jiang J, Feng H, Ghirlando R, Xiao TS, Bai Y. 2015. Structural mechanisms of nucleosome recognition by linker histones. Mol. Cell 59:628–38
    [Google Scholar]
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