Chromatin polymorphism and the nucleosome superfamily: A genealogy

Cell Cycle

Volumn 6, Issue 17, 2007, Pages 2113-2119

  Lavelle, Christophe ^a   Prunell, Ariel ^b  

^a INSTITUT GUSTAVE ROUSSY   (France)

^b INSTITUT JACQUES MONOD   (France)

Author keywords

Altosome; Chromatin; Chromatosome; Hexasome; Histone variants; Lexosome; Nucleosome; Remodeling; Reversome; Tetrasome

Indexed keywords

HIGH MOBILITY GROUP A PROTEIN; HIGH MOBILITY GROUP B PROTEIN; HIGH MOBILITY GROUP N PROTEIN; HISTONE H2AX; HISTONE H2AZ; NUCLEOSOME ASSEMBLY PROTEIN 1; NUCLEOSOME ASSEMBLY PROTEIN 2; RNA POLYMERASE II; UNCLASSIFIED DRUG;

AFFINITY CHROMATOGRAPHY; ATOMIC FORCE MICROSCOPY; CARBOXY TERMINAL SEQUENCE; CELL CYCLE; CHROMATIN; DNA CLEAVAGE; ELECTRON MICROSCOPY; GENEALOGY; GENETIC POLYMORPHISM; HUMAN; NUCLEOSOME; RADIATION SCATTERING; REVIEW;

EID: 34548829891     PISSN: 15384101     EISSN: 15514005     Source Type: Journal    
DOI: 10.4161/cc.6.17.4631     Document Type: Review

References (147)

1. Bancaud A, Conde e Silva N, Barbi M, Wagner G, Allemand JF, Mozziconacci J, Lavelle C, Croquette V, Victor JM, Prunell A, Viovy JL. Structural plasticity of single chromatin fibers revealed by torsional manipulation. Nat Struct Mol Biol 2006; 13:444-50.
2. Bancaud A, Wagner G, Conde e Silva N, Lavelle C, Wong H, Mozziconacci J, Barbi M, Sivolob A, Le Cam E, Mouawad L, Viovy JL, Victor JM, Prunell A. Nucleosome chiral transition under positive torsional stress in single chromatin fibers. Mol Cell 2007; 27:135-47.
3. Flemming W. Zell substanz, kern und zelltheilung. Leipzig: Vogel, 1882.
4. Kossel A. Z physiol Chem 1884; 511-5.
5. Kornberg RD. Chromatin structure: A repeating unit of histones and DNA. Science 1974; 184:868-71.
6. Noll M. Subunit structure of chromatin. Nature 1974; 251:249-51.
7. Olins AL, Olins DE. Spheroid chromatin units (v bodies). Science 1974; 183:330-2.
8. Kornberg RD, Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 1999; 98:285-94.
9. Olins DE, Olins AL. Chromatin history: Our view from the bridge. Nat Rev Mol Cell Biol 2003; 4:809-14.
10. Oudet P, Gross-Bellard M, Chambon P. Electron microscopic and biochemical evidence that chromatin structure is a repeating unit. Cell 1975; 4:281-300.
11. Benecke A. Chromatin code, local nonequilibrium dynamics, and the emergence of transcription regulatory programs. Eur Phys J E Soft Matter 2006; 19:353-66.
12. Cosgrove MS, Wolberger C. How does the histone code work? Biochem Cell Biol 2005; 83:468-76.
13. Jenuwein T, Allis CD. Translating the histone code. Science 2001; 293:1074-80.
14. Turner BM. Histone acetylation and an epigenetic code. Bioessays 2000; 22:836-45.
15. Tomschik M, Karymov MA, Zlatanova J, Leuba SH. The archaeal histone-fold protein HMf organizes DNA into bona fide chromatin fibers. Structure 2001; 9:1201-11.
16. Zlatanova J, Seebart C, Tomschik M. Nap1: Taking a closer look at a juggler protein of extraordinary skills. Faseb J 2007; 21:1294-310.
17. Simpson RT. Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry 1978; 17:5524-31.
18. Hamiche A, Schultz P, Ramakrishnan V, Oudet P, Prunell A. Linker histone-dependent DNA structure in linear mononucleosomes. J Mol Biol 1996; 257:30-42.
19. Sivolob A, Prunell A. Linker histone-dependent organization and dynamics of nucleosome entry/exit DNAs. J Mol Biol 2003; 331:1025-40.
20. Kepert JF, Mazurkiewicz J, Heuvelman GL, Toth KF, Rippe K. NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformation. J Biol Chem 2005; 280:34063-72.
21. Kysela B, Chovanec M, Jeggo PA. Phosphorylation of linker histones by DNA-dependent protein kinase is required for DNA ligase IV-dependent ligation in the presence of histone H1. Proc Natl Acad Sci USA 2005; 102:1877-82.
22. O'Neill TE, Meersseman G, Pennings S, Bradbury EM. Deposition of histone H1 onto reconstituted nucleosome arrays inhibits both initiation and elongation of transcripts by T7 RNA polymerase. Nucleic Acids Res 1995; 23:1075-82.
23. Shimamura A, Sapp M, Rodriguez-Campos A, Worcel A. Histone H1 represses transcription from minichromosomes assembled in vitro. Mol Cell Biol 1989; 9:5573-84.
24. Wolffe AP. Dominant and specific repression of Xenopus oocyte 5S RNA genes and satellite I DNA by histone H1. Embo J 1989; 8:527-37.
25. Zlatanova J, Caiafa P, Van Holde K. Linker histone binding and displacement: Versatile mechanism for transcriptional regulation. Faseb J 2000; 14:1697-704.
26. Bednar J, Horowitz RA, Grigoryev SA, Carruthers LM, Hansen JC, Koster AJ, Woodcock CL. Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci USA 1998; 95:14173-8.
27. Hannon R, Bateman E, Allan J, Harborne N, Gould H. Control of RNA polymerase binding to chromatin by variations in linker histone composition. J Mol Biol 1984; 180:131-49.
28. Thomas JO. Histone H1: Location and role. Curr Opin Cell Biol 1999; 11:312-7.
29. Woodcock CL, Skoultchi AI, Fan Y. Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length. Chromosome Res 2006; 14:17-25.
30. Misteli T, Gunjan A, Hock R, Bustin M, Brown DT. Dynamic binding of histone H1 to chromatin in living cells. Nature 2000; 408:877-81.
31. Catez F, Brown DT, Misteli T, Bustin M. Competition between histone H1 and HMGN proteins for chromatin binding sites. EMBO Rep 2002; 3:760-6.
32. Catez F, Yang H, Tracey KJ, Reeves R, Misteli T, Bustin M. Network of dynamic interactions between histone H1 and high-mobility-group proteins in chromatin. Mol Cell Biol 2004; 24:4321-8.
33. Burgoyne LA, Skinner JD. Chromatin superstructure: The next level of structure above the nucleosome has an alternating character: A two-nucleosome based series is generated by probes armed with DNAase-I acting on isolated nuclei. Biochem Biophys Res Commun 1981; 99:893-9.
34. Khachatrian AT, Pospelov VA, Svetlikova SB, Vorob'ev VI. Nucleodisome - A new repeat unit of chromatin revealed in nuclei of pigeon erythrocytes by DNase I digestion. FEBS Lett 1981; 128:90-2.
35. Kukushkin AN, Svetlikova SB, Pospelov VA. A structure of potentially active and inactive genes of chicken erythrocyte chromatin upon decondensation. Nucleic Acids Res 1988; 16:8555-69.
36. Pospelov VA, Svetlikova SB. Higher order chromatin structure determines double-nucleosome periodicity of DNA fragmentation. Mol Biol Rep 1982; 8:117-22.
37. Pospelov VA, Svetlikova SB. On the mechanism of nucleodisome splitting off by nucleases. FEBS Lett 1982; 146:157-60.
38. Drinkwater RD, Wilson PJ, Skinner JD, Burgoyne LA. Chromatin structures: Dissecting their mixed patterns in nuclease digests. Nucleic Acids Res 1987; 15:8087-103.
39. Prior CP, Cantor CR, Johnson EM, Littau VC, Allfrey VG. Reversible changes in nucleosome structure and histone H3 accessibility in transcriptionally active and inactive states of rDNA chromatin. Cell 1983; 34:1033-42.
40. Chen TA, Allfrey VG. Rapid and reversible changes in nucleosome structure accompany the activation, repression, and superinduction of murine fibroblast protooncogenes c-fos and c-myc. Proc Natl Acad Sci USA 1987; 84:5252-6.
41. Johnson EM, Sterner R, Allfrey VG. Altered nucleosomes of active nucleolar chromatin contain accessible histone H3 in its hyperacetylated forms. J Biol Chem 1987; 262:6943-6.
42. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997; 389:251-60.
43. Olins DE, Bryan PN, Harrington RE, Hill WE, Olins AL. Conformational states of chromatin nu bodies induced by urea. Nucleic Acids Res 1977; 4:1911-31.
44. Bazett-Jones DP, Mendez E, Czarnota GJ, Ottensmeyer FP, Allfrey VG. Visualization and analysis of unfolded nucleosomes associated with transcribing chromatin. Nucleic Acids Res 1996; 24:321-9.
45. Protacio RU, Widom J. Nucleosome transcription studied in a real-time synchronous system: Test of the lexosome model and direct measurement of effects due to histone octamer. J Mol Biol 1996; 256:458-72.
46. Camerini-Otero RD, Sollner-Webb B, Felsenfeld G. The organization of histones and DNA in chromatin: Evidence for an arginine-rich histone kernel. Cell 1976; 8:333-47.
47. Oudet P, Germond JE, Sures M, Gallwitz D, Bellard M, Chambon P. Nucleosome structure I: All four histones, H2A, H2B, H3, and H4, are required to form a nucleosome, but an H3-H4 subnucleosomal particle is formed with H3-H4 alone. Cold Spring Harb Symp Quant Biol 1978; 42(Pt 1):287-300.
48. Bina-Stein M. Folding of 140-base pair length DNA by a core of arginine-rich histones. J Biol Chem 1978; 253:5213-9.
49. Read CM, Crane-Robinson C. The structure of sub-nucleosomal particles: The octameric (H3/H4)4-125-base-pair-DNA complex. Eur J Biochem 1985; 152:143-50.
50. Baxevanis AD, Godfrey JE, Moudrianakis EN. Associative behavior of the histone (H3-H4)2 tetramer: Dependence on ionic environment. Biochemistry 1991; 30:8817-23.
51. Simon RH, Camerini-Otero RD, Felsenfeld G. An octamer of histones H3 and H4 forms a compact complex with DNA of nucleosome size. Nucleic Acids Res 1978; 5:4805-18.
52. Moss T, Stephens RM, Crane-Robinson C, Bradbury EM. A nucleosome-like structure containing DNA and the arginine-rich histones H3 and H4. Nucleic Acids Res 1977; 4:2477-85.
53. Alilat M, Sivolob A, Revet B, Prunell A. Nucleosome dynamics: Protein and DNA contributions in the chiral transition of the tetrasome, the histone (H3-H4)2 tetramer-DNA particle. J Mol Biol 1999; 291:815-41.
54. Flaus A, Luger K, Tan S, Richmond TJ. Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals. Proc Natl Acad Sci USA 1996; 93:1370-5.
55. Aragay AM, Diaz P, Daban JR. Association of nucleosome core particle DNA with different histone oligomers: Transfer of histones between DNA-(H2A,H2B) and DNA-(H3,H4) complexes. J Mol Biol 1988; 204:141-54.
56. Hamiche A, Carot V, Alilat M, De Lucia F, O'Donohue MF, Revet B, Prunell A. Interaction of the histone (H3-H4)2 tetramer of the nucleosome with positively supercoiled DNA minicircles: Potential flipping of the protein from a left- to a right-handed superhelical form. Proc Natl Acad Sci USA 1996; 93:7588-93.
57. Sivolob A, De Lucia F, Alilat M, Prunell A. Nucleosome dynamics. VI. Histone tail regulation of tetrasome chiral transition: A relaxation study of tetrasomes on DNA minicircles. J Mol Biol 2000; 295:55-69.
58. Sivolob A, Prunell A. Nucleosome dynamics V. Ethidium bromide versus histone tails in modulating ethidium bromide-driven tetrasome chiral transition: A fluorescence study of tetrasomes on DNA minicircles. J Mol Biol 2000; 295:41-53.
59. Sivolob A, Prunell A. Nucleosome conformational flexibility and implications for chromatin dynamics. Philos Transact A Math Phys Eng Sci 2004; 362:1519-47.
60. Sandman K, Reeve JN. Structure and functional relationships of archaeal and eukaryal histones and nucleosomes. Arch Microbiol 2000; 173:165-9.
61. Kireeva ML, Walter W, Tchernajenko V, Bondarenko V, Kashlev M, Studitsky VM. Nucleosome remodeling induced by RNA polymerase II: Loss of the H2A/H2B dimer during transcription. Mol Cell 2002; 9:541-52.
62. de la Escalera S, Nieto MA, Palacian E. Preparation and structural characterization of nucleosomal core particles lacking one H2A.H2B dimer. Biochem Biophys Res Commun 1988; 157:541-7.
63. Read CM, Baldwin JP, Crane-Robinson C. Structure of subnucleosomal particles: Tetrameric (H3/H4)2 146 base pair DNA and hexameric (H3/H4)2(H2A/H2B)1 146 base pair DNA complexes. Biochemistry 1985; 24:4435-50.
64. Conde e Silva N, Black BE, Sivolob A, Filipski J, Cleveland DW, Prunell A. CENP-A-containing nucleosomes: Easier disassembly versus exclusive centromeric localization. J Mol Biol 2007; 370:555-73.
65. Mazurkiewicz J, Kepert JF, Rippe K. On the mechanism of nucleosome assembly by histone chaperone NAP1. J Biol Chem 2006; 281:16462-72.
66. Baer BW, Rhodes D. Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes. Nature 1983; 301:482-8.
67. Gonzalez PJ, Palacian E. Interaction of RNA polymerase II with structurally altered nucleosomal particles: Transcription is facilitated by loss of one H2A.H2B dimer. J Biol Chem 1989; 264:18457-62.
68. O'Donohue MF, Duband-Goulet I, Hamiche A, Prunell A. Octamer displacement and redistribution in transcription of single nucleosomes. Nucleic Acids Res 1994; 22:937-45.
69. Studitsky VM, Clark DJ, Felsenfeld G. A histone octamer can step around a transcribing polymerase without leaving the template. Cell 1994; 76:371-82.
70. Lavelle C. Transcription elongation through a chromatin template. Biochimie 2007; 89:516-27.
71. Groth A, Rocha W, Verreault A, Almouzni G. Chromatin challenges during DNA replication and repair. Cell 2007; 128:721-33.
72. van Attikum H, Gasser SM. ATP-dependent chromatin remodeling and DNA double-strand break repair. Cell Cycle 2005; 4:1011-4.
73. Jamai A, Imoberdorf RM, Strubin M. Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol Cell 2007; 25:345-55.
74. Benedict RC, Moudrianakis EN, Ackers GK. Interactions of the nucleosomal core histones: A calorimetric study of octamer assembly. Biochemistry 1984.
75. Sivolob A, Lavelle C, Prunell A. Sequence-dependent nucleosome structural and dynamic polymorphism: Potential involvement of histone H2B N-terminal tail proximal domain. J Mol Biol 2003; 326:49-63.
76. Mozziconacci J, Victor JM. Nucleosome gaping supports a functional structure for the 30 nm chromatin fiber. J Struct Biol 2003; 143:72-6.
77. Mozziconacci J, Lavelle C, Barbi M, Lesne A, Victor JM. A physical model for the condensation and decondensation of eukaryotic chromosomes. FEBS Lett 2006; 580:368-72.
78. Huyen Y, Zgheib O, Ditullio Jr RA, Gorgoulis VG, Zacharatos P, Petty TJ, Sheston EA, Mellert HS, Stavridi ES, Halazonetis TD. Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 2004; 432:406-11.
79. Lorch Y, Cairns BR, Zhang M, Kornberg RD. Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell 1998; 94:29-34.
80. Schnitzler G, Sif S, Kingston RE. Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell 1998; 94:17-27.
81. Schnitzler GR, Cheung CL, Hafner JH, Saurin AJ, Kingston RE, Lieber CM. Direct imag- imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips. Mol Cell Biol 2001; 21:8504-11.
82. Ulyanova NP, Schnitzler GR. Human SWI/SNF generates abundant, structurally altered dinucleosomes on polynucleosomal templates. Mol Cell Biol 2005; 25:11156-70.
83. Lorch Y, Zhang M, Kornberg RD. RSC unravels the nucleosome. Mol Cell 2001; 7:89-95.
84. Ulyanova NP, Schnitzler GR. Inverted factor access and slow reversion characterize SWI/SNF-altered nucleosome dimers. J Biol Chem 2007; 282:1018-28.
85. Tatchell K, Van Holde KE. Compact oligomers and nucleosome phasing. Proc Natl Acad Sci USA 1978; 75:3583-7.
86. De Lucia F, Alilat M, Sivolob A, Prunell A. Nucleosome dynamics. III. Histone tail-dependent fluctuation of nucleosomes between open and closed DNA conformations. Implications for chromatin dynamics and the linking number paradox: A relaxation study of mononucleosomes on DNA minicircles. J Mol Biol 1999; 285:1101-19.
87. Prunell A, Sivolob A. Paradox lost: Nucleosome structure and dynamics by the DNA minicircle approach. Chromatin structure and dynamics: State-of-the-art. Amsterdam: Elsevier Science, 2004:45-73.
88. Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 1987; 84:7024-7.
89. Salceda J, Fernandez X, Roca J. Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA. Embo J 2006; 25:2575-83.
90. Borun TW, Ajiro K, Zweidler A, Dolby TW, Stephens RE. Studies of human histone messenger RNA. II. The resolution of fractions containing individual human histone messenger RNA species. J Biol Chem 1977; 252:173-80.
91. Kamakaka RT, Biggins S. Histone variants: Deviants? Genes Dev 2005; 19:295-310.
92. Wolffe AP, Pruss D. Deviant nucleosomes: The functional specialization of chromatin. Trends Genet 1996; 12:58-62.
93. Bernstein E, Hake SB. The nucleosome: A little variation goes a long way. Biochem Cell Biol 2006; 84:505-17.
94. Jin J, Cai Y, Li B, Conaway RC, Workman JL, Conaway JW, Kusch T. In and out: Histone variant exchange in chromatin. Trends Biochem Sci 2005; 30:680-7.
95. Sarma K, Reinberg D. Histone variants meet their match. Nat Rev Mol Cell Biol 2005; 6:139-49.
96. Malik HS, Henikoff S. Phylogenomics of the nucleosome. Nat Struct Biol 2003; 10:882-91.
97. Pusarla RH, Bhargava P. Histones in functional diversification: Core histone variants. Febs J 2005; 272:5149-68.
98. West MH, Bonner WM. Histone 2A, a heteromorphous family of eight protein species. Biochemistry 1980; 19:3238-45.
99. Redon C, Pilch D, Rogakou E, Sedelnikova O, Newrock K, Bonner W. Histone H2A variants H2AX and H2AZ. Curr Opin Genet Dev 2002; 12:162-9.
100. Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J Biol Chem 1998; 273:5858-68.
101. Pehrson JR, Fried VA. MacroH2A, a core histone containing a large nonhistone region. Science 1992; 257:1398-400.
102. Chadwick BP, Willard HF. Histone H2A variants and the inactive X chromosome: Identification of a second macroH2A variant. Hum Mol Genet 2001; 10:1101-13.
103. Chadwick BP, Willard HF. A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome. J Cell Biol 2001; 152:375-84.
104. Gineitis AA, Zalenskaya IA, Yau PM, Bradbury EM, Zalensky AO. Human sperm telomere-binding complex involves histone H2B and secures telomere membrane attachment. J Cell Biol 2000; 151:1591-8.
105. Zalensky AO, Siino JS, Gineitis AA, Zalenskaya IA, Tomilin NV, Yau P, Bradbury EM. Human testis/sperm-specific histone H2B (hTSH2B): Molecular cloning and characterization. J Biol Chem 2002; 277:43474-80.
106. Churikov D, Siino J, Svetlova M, Zhang K, Gineitis A, Morton Bradbury E, Zalensky A. Novel human testis-specific histone H2B encoded by the interrupted gene on the X chromosome. Genomics 2004; 84:745-56.
107. Tagami H, Ray-Gallet D, Almouzni G, Nakatani Y. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 2004; 116:51-61.
108. Henikoff S, Dalal Y. Centromeric chromatin: What makes it unique? Curr Opin Genet Dev 2005; 15:177-84.
109. Earnshaw WC, Rothfield N. Identification of a family of human centromere proteins using autoimmune sera from patients with scleroderma. Chromosoma 1985; 91:313-21.
110. Palmer DK, O'Day K, Wener MH, Andrews BS, Margolis RL. A 17-kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones. J Cell Biol 1987; 104:805-15.
111. Meluh PB, Yang P, Glowczewski L, Koshland D, Smith MM. Cse4p is a component of the core centromere of Saccharomyces cerevisiae. Cell 1998; 94:607-13.
112. Stoler S, Keith KC, Curnick KE, Fitzgerald-Hayes M. A mutation in CSE4, an essential gene encoding a novel chromatin-associated protein in yeast, causes chromosome nondisjunction and cell cycle arrest at mitosis. Genes Dev 1995; 9:573-86.
113. Henikoff S, Ahmad K, Platero JS, van Steensel B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci USA 2000; 97:716-21.
114. Wisniewski JR, Zougman A, Kruger S, Mann M. 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 Proteomics 2007; 6:72-87.
115. Zlatanova J, Doenecke D. Histone H1 zero: A major player in cell differentiation? Faseb J 1994; 8:1260-8.
116. Bao Y, Konesky K, Park YJ, Rosu S, Dyer PN, Rangasamy D, Tremethick DJ, Laybourn PJ, Luger K. Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. Embo J 2004; 23:3314-24.
117. Doyen CM, Montel F, Gautier T, Menoni H, Claudet C, Delacour-Larose M, Angelov D, Hamiche A, Bednar J, Faivre-Moskalenko C, Bouvet P, Dimitrov S. Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome. Embo J 2006; 25:4234-44.
118. Park YJ, Dyer PN, Tremethick DJ, Luger K. A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome. J Biol Chem 2004; 279:24274-82.
119. Meneghini MD, Wu M, Madhani HD. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 2003; 112:725-36.
120. Jin C, Felsenfeld G. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev 2007; 21:1519-29.
121. Mito Y, Henikoff JG, Henikoff S. Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet 2005; 37:1090-7.
122. Ahmad K, Henikoff S. Histone H3 variants specify modes of chromatin assembly. Proc Natl Acad Sci USA 2002; 99(Suppl 4):16477-84.
123. Bruce K, Myers FA, Mantouvalou E, Lefevre P, Greaves I, Bonifer C, Tremethick DJ, Thorne AW, Crane-Robinson C. The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken. Nucleic Acids Res 2005; 33:5633-9.
124. Billett MA, Hindley J. A study of the quantitative variation of histones, and their relationship to RNA synthesis, during erythropoiesis in the adult chicken. Eur J Biochem 1972; 28:451-62.
125. Fan JY, Gordon F, Luger K, Hansen JC, Tremethick DJ. The essential histone variant H2A. Z regulates the equilibrium between different chromatin conformational states. Nat Struct Biol 2002; 9:172-6.
126. Loyola A, Almouzni G. Histone chaperones, a supporting role in the limelight. Biochim Biophys Acta 2004; 1677:3-11.
127. Philpott A, Krude T, Laskey RA. Nuclear chaperones. Semin Cell Dev Biol 2000; 11:7-14.
128. Laskey RA, Honda BM, Mills AD, Finch JT. Nucleosomes are assembled by an acidic protein which binds histones and transfers them to DNA. Nature 1978; 275:416-20.
129. Kleinschmidt JA, Fortkamp E, Krohne G, Zentgraf H, Franke WW. Coexistence of two different types of soluble histone complexes in nuclei of Xenopus laevis oocytes. J Biol Chem 1985; 260:1166-76.
130. Luk E, Vu ND, Patteson K, Mizuguchi G, Wu WH, Ranjan A, Backus J, Sen S, Lewis M, Bai Y, Wu C. Chz1, a nuclear chaperone for histone H2AZ. Mol Cell 2007; 25:357-68.
131. Orphanides G, LeRoy G, Chang CH, Luse DS, Reinberg D. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 1998; 92:105-16.
132. Smith S, Stillman B. Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro. Cell 1989; 58:15-25.
133. Lamour V, Lecluse Y, Desmaze C, Spector M, Bodescot M, Aurias A, Osley MA, Lipinski M. A human homolog of the S. cerevisiae HIR1 and HIR2 transcriptional repressors cloned from the DiGeorge syndrome critical region. Hum Mol Genet 1995; 4:791-9.
134. Furuyama T, Dalal Y, Henikoff S. Chaperone-mediated assembly of centromeric chromatin in vitro. Proc Natl Acad Sci USA 2006; 103:6172-7.
135. Vermaak D, Wade PA, Jones PL, Shi YB, Wolffe AP. Functional analysis of the SIN3-histone deacetylase RPD3-RbAp48-histone H4 connection in the Xenopus oocyte. Mol Cell Biol 1999; 19:5847-60.
136. Polo SE, Almouzni G. Chromatin assembly: A basic recipe with various flavours. Curr Opin Genet Dev 2006; 16:104-11.
137. Tyler JK. Chromatin assembly: Cooperation between histone chaperones and ATP-dependent nucleosome remodeling machines. Eur J Biochem 2002; 269:2268-74.
138. Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 2004; 303:343-8.
139. Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates IIIrd JR, Abmayr SM, Washburn MP, Workman JL. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 2004; 306:2084-7.
140. Camahort R, Li B, Florens L, Swanson SK, Washburn MP, Gerton JL. Scm3 is essential to recruit the histone H3 variant cse4 to centromeres and to maintain a functional kinetochore. Mol Cell 2007.
141. Mizuguchi G, Xiao H, Wisniewski J, Smith MM, Wu C. Nonhistone Scm3 and histones CenH3-H4 assemble the core of centromere-specific nucleosomes. Cell 2007; 129:1153-64.
142. Stoler S, Rogers K, Weitze S, Morey L, Fitzgerald-Hayes M, Baker RE. Scm3, an essential Saccharomyces cerevisiae centromere protein required for G2/M progression and Cse4 localization. Proc Natl Acad Sci USA 2007; 104:10571-6.
143. Flaus A, Owen-Hughes T. Mechanisms for ATP-dependent chromatin remodelling: Farewell to the tuna-can octamer? Curr Opin Genet Dev 2004; 14:165-73.
144. Dalal Y, Wang H, Lindsay S, Henikoff S. Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biology 2007; 5:e218.
145. Weintraub H, Worcel A, Alberts B. A model of chromatin based upon two symmetrically paired half-nucleosomes. Cell 1976; 9:409-17.
146. Oudet P, Germond JE, Bellard M, Spadafora C, Chambon P. Nucleosome structure. Philos Trans R Soc Lond B Biol Sci 1978; 283:241-58.
147. Tatchell K, Van Holde KE. Reconstitution of chromatin core particles. Biochemistry 1977; 16:5295-303.