The Nucleosome: From Genomic Organization to Genomic Regulation

Cell

Volumn 116, Issue 2, 2004, Pages 259-272

  Khorasanizadeh, Sepideh ^a  

^a UNIVERSITY OF VIRGINIA HEALTH SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; ARGININE; DNA; HISTONE; LYSINE; SERINE;

ACETYLATION; AMINO ACID SEQUENCE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CHROMATIN; DNA BINDING; DNA DETERMINATION; DNA METHYLATION; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; ELECTRON; GENE CONTROL; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOMICS; HUMAN; METHYLATION; NONHUMAN; NUCLEOSOME; PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STRUCTURE; REGULATORY MECHANISM; REVIEW; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION; UBIQUITINATION;

EUKARYOTA;

EID: 0842324785     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(04)00044-3     Document Type: Review

References (98)

1. Aasland R., Stewart A.F., Gibson T. The SANT domain. a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB Trends Biochem. Sci. 21:1996;87-88.
2. Agalioti T., Chen G., Thanos D. Deciphering the transcriptional histone acetylation code for a human gene. Cell. 111:2002;381-392.
3. Ahmad K., Henikoff S. Centromeres are specialized replication domains in heterochromatin. J. Cell Biol. 153:2001;101-110.
4. Ahmad K., Henikoff S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell. 9:2002;1191-1200.
5. Allen M.D., Buckle A.M., Cordell S.C., Lowe J., Bycroft M. The crystal structure of AF1521 a protein from Archaeoglobus fulgidus with homology to the non-histone domain of macroH2A. J. Mol. Biol. 330:2003;503-511.
6. Arents G., Burlingame R.W., Wang B.C., Love W.E., Moudrianakis E.N. The nucleosomal core histone octamer at 3.1 Å resolution. a tripartite protein assembly and a left-handed superhelix Proc. Natl. Acad. Sci. USA. 88:1991;10148-10152.
7. Asturias F.J., Chung W.H., Kornberg R.D., Lorch Y. Structural analysis of the RSC chromatin-remodeling complex. Proc. Natl. Acad. Sci. USA. 99:2002;13477-13480.
8. Bakayev V.V., Bakayeva T.G., Varshavsky A.J. Nucleosomes and subnucleosomes. heterogeneity and composition Cell. 11:1977;619-629.
9. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature. 410:2001;120-124.
10. Bannister A.J., Schneider R., Kouzarides T. Histone methylation. dynamic or static? Cell. 109:2002;801-806.
11. Bednar J., Horowitz R.A., Grigoryev S.A., Carruthers L.M., Hansen J.C., Koster A.J., Woodcock C.L. 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. 95:1998;14173-14178.
12. Beisel C., Imhof A., Greene J., Kremmer E., Sauer F. Histone methylation by the Drosophila epigenetic transcriptional regulator Ash1. Nature. 419:2002;857-862.
13. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 16:2002;6-21.
14. Boeger H., Griesenbeck J., Strattan J.S., Kornberg R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell. 11:2003;1587-1598.
15. Caruthers J.M., Johnson E.R., McKay D.B. Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase. Proc. Natl. Acad. Sci. USA. 97:2000;13080-13085.
16. Chadwick B.P., Willard H.F. A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome. J. Cell Biol. 152:2001;375-384.
17. Cheng X., Roberts R.J. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 29:2001;3784-3795.
18. Cheung P., Allis C.D., Sassone-Corsi P. Signaling to chromatin through histone modifications. Cell. 103:2000;263-271.
19. Clements A., Poux A.N., Lo W.S., Pillus L., Berger S.L., Marmorstein R. Structural basis for histone and phosphohistone binding by the GCN5 histone acetyltransferase. Mol. Cell. 12:2003;461-473.
20. Costanzi C., Pehrson J.R. Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature. 393:1998;599-601.
21. Cui Y., Bustamante C. Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc. Natl. Acad. Sci. USA. 97:2000;127-132.
22. Daniel, J.A., Torok, M.S., Sun, Z.W., Schieltz, D., Allis, C.D., Yates, J.R., and Grant, P.A. (2003). Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J. Biol. Chem., in press. Published online December 3, 2003. 10.1074/jbc.C300494200 .
23. Davey C.A., Sargent D.F., Luger K., Maeder A.W., Richmond T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319:2002;1097-1113.
24. Dhalluin C., Carlson J.E., Zeng L., He C., Aggarwal A.K., Zhou M.-M. Structure and ligand of a histone acetyltransferase bromodomain. Nature. 399:1999;491-496.
25. Dou Y., Bowen J., Liu Y., Gorovsky M.A. Phosphorylation and an ATP-dependent process increase the dynamic exchange of H1 in chromatin. J. Cell Biol. 158:2002;1161-1170.
26. Fan H.Y., He X., Kingston R.E., Narlikar G.J. Distinct strategies to make nucleosomal DNA accessible. Mol. Cell. 11:2003;1311-1322. a.
27. Fan Y., Nikitina T., Morin-Kensicki E.M., Zhao J., Magnuson T.R., Woodcock C.L., Skoultchi A.I. H1 linker histones are essential for mouse development and affect nucleosome spacing in vivo. Mol. Cell. Biol. 23:2003;4559-4572. b.
28. Fazzio T.G., Tsukiyama T. Chromatin remodeling in vivo. evidence for a nucleosome sliding mechanism Mol. Cell. 12:2003;1333-1340.
29. Finch J.T., Klug A. Solenoidal model for superstructure in chromatin. Proc. Natl. Acad. Sci. USA. 73:1976;1897-1901.
30. Fischle W., Wang Y., Jacobs S.A., Kim Y., Allis C.D., Khorasanizadeh S. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17:2003;1870-1881. a.
31. Fischle W., Wang Y., Allis L.D. Binary switches and modification cassettes in histone biology and beyond. Nature. 425:2003;475-479. b.
32. Flaus A., Owen-Hughes T. Mechanisms for nucleosome mobilization. Biopolymers. 68:2003;563-578.
33. Fuks F., Hurd P.J., Wolf D., Nan X., Bird A.P., Kouzarides T. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J. Biol. Chem. 278:2003;4035-4040.
34. Grune T., Brzeski J., Eberharter A., Clapier C.R., Corona D.F., Becker P.B., Muller C.W. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell. 12:2003;449-460.
35. Guarente L. Sir2 links chromatin silencing, metabolism, and aging. Genes Dev. 14:2000;1021-1026.
36. Harp J.M., Hanson B.L., Timm D.E., Bunick G.J. Asymmetries in the nucleosome core particle at 2.5 angstrom resolution. Acta Crystallogr. D. 56:2000;1513-1534.
37. Harp J.M., Uberbacher E.C., Roberson A.E., Palmer E.L., Gewiess A., Bunick G.J. X-ray diffraction analysis of crystals containing twofold symmetric nucleosome core particles. Acta Crystallogr. D. 52:1996;283-288.
38. Hassan A.H., Prochasson P., Neely K.E., Galasinski S.C., Chandy M., Carrozza M.J., Workman J.L. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell. 111:2002;369-379.
39. Henry K.W., Wyce A., Lo W.S., Duggan L.J., Emre N.C., Kao C.F., Pillus L., Shilatifard A., Osley M.A., Berger S.L. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 17:2003;2648-2663.
40. Hewish D.R., Burgoyne L.A. Chromatin sub-structure. The digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease. Biochem. Biophys. Res. Commun. 52:1973;504-510.
41. Hsu J.Y., Sun Z.W., Li X., Reuben M., Tatchell K., Bishop D.K., Grushcow J.M., Brame C.J., Caldwell J.A., Hunt D.F.et al. Mitotic phosphorylation of histone H3 is governed by Ipl1/aurora kinase and Glc7/PP1 phosphatase in budding yeast and nematodes. Cell. 102:2000;279-291.
42. Jacobs S.A., Khorasanizadeh S. Structure of the HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science. 295:2002;2080-2083.
43. Jacobs S.A., Taverna S.D., Zhang Y., Briggs S.D., Li J., Eissenberg J.C., Allis C.D., Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 20:2001;5232-5241.
44. II250 double bromodomain module. Science. 288:2000;1422-1425.
45. Kassabov S.R., Zhang B., Persinger J., Bartholomew B. SWI/SNF unwraps, slides, and rewraps the nucleosome. Mol. Cell. 11:2003;391-403.
46. Khochbin S. Histone H1 diversity. bridging regulatory signals to linker histone function Gene. 271:2001;1-12.
47. Kornberg R.D. Chromatin structure. a repeating unit of histones and DNA Science. 184:1974;868-871.
48. Kurdistani S.K., Grunstein M. Histone acetylation and deacetylation in yeast. Nat. Rev. Mol. Cell Biol. 4:2003;276-284.
49. Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature. 410:2001;116-120.
50. Lachner M., O'Sullivan R.J., Jenuwein T. An epigenetic road map for histone lysine methylation. J. Cell Sci. 116:2003;2117-2124.
51. Luger K., Maeder A.W., Richmond R.K., Sargent D.F., Richmond T.J. X-ray structure of the nucleosome core particle at 2.8 A resolution. Nature. 389:1997;251-259.
52. Marmorstein R. Structure and function of histone acetyltransferases. Cell. Mol. Life Sci. 58:2001;693-703. a.
53. Marmorstein R. Structure of histone deacetylases. insights into substrate recognition and catalysis Structure (Camb). 9:2001;1127-1133. b.
54. Min J., Feng Q., Li Z., Zhang Y., Xu R.M. Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell. 112:2003;711-723. a.
55. Min J., Zhang Y., Xu R.M. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev. 17:2003;1823-1828. b.
56. Misteli T., Gunjan A., Hock R., Bustin M., Brown D.T. Dynamic binding of histone H1 to chromatin in living cells. Nature. 408:2000;877-881.
57. Mizuguchi, G., Shen, X., Landry, J., Wu, W.H., Sen, S., and Wu, C. (2003). ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science, in press. Published online November 26, 2003. 10.1126/science.1090701 .
58. Narlikar G.J., Fan H.Y., Kingston R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell. 108:2002;475-487.
59. Nielsen P.R., Nietlispach D., Mott H.R., Callaghan J., Bannister A., Kouzarides T., Murzin A.G., Murzina N.V., Laue E.D. Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature. 416:2002;103-107.
60. Noll M., Kornberg R.D. Action of micrococcal nuclease on chromatin and the location of histone H1. J. Mol. Biol. 109:1977;393-404.
61. Ohki I., Shimotake N., Fujita N., Jee J., Ikegami T., Nakao M., Shirakawa M. Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell. 105:2001;487-497.
62. Okamoto, I., Otte, A.P., Allis, C.D., Reinberg, D., and Heard, E. (2003). Epigenetic dynamics of imprinted X inactivation during early mouse development. Science, in press. Published online December 17, 2003. 10.1126/science.1092727 .
63. Olins A.L., Olins D.E. Spheroid chromatin units (v bodies). Science. 183:1974;330-332.
64. Olins D.E., Olins A.L. Chromatin history. our view from the bridge Nat. Rev. Mol. Cell Biol. 4:2003;809-814.
65. Oudet P., Gross-Bellard M., Chambon P. Electron microscopic and biochemical evidence that chromatin structure is a repeating unit. Cell. 4:1975;281-300.
66. Owen D.J., Ornaghi P., Yang J., Lowe N., Evans P.R., Ballario P., Neuhaus D., Filetici P., Travers A.A. The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase Gcn5p. EMBO J. 19:2000;6141-6149.
67. Park J.H., Cosgrove M.S., Youngman E., Wolberger C., Boeke J.D. A core nucleosome surface crucial for transcriptional silencing. Nat. Genet. 32:2002;273-279.
68. Ramachandran A., Omar M., Cheslock P., Schnitzler G.R. Linker histone H1 modulates nucleosome remodeling by human SWI/SNF. J. Biol. Chem. 278:2003;48590-48601.
69. Ramakrishnan V., Finch J.T., Graziano V., Lee P.L., Sweet R.M. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature. 362:1993;219-223.
70. Richmond T.J., Davey C.A. The structure of DNA in the nucleosome core. Nature. 423:2003;145-150.
71. Richmond T.J., Finch J.T., Rushton B., Rhodes D., Klug A. Structure of the nucleosome core particle at 7 A resolution. Nature. 311:1984;532-537.
72. Richmond T.J., Searles M.A., Simpson R.T. Crystals of a nucleosome core particle containing defined sequence DNA. J. Mol. Biol. 199:1988;161-170.
73. Rogakou E.P., Pilch D.R., Orr A.H., Ivanova V.S., Bonner W.M. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J. Biol. Chem. 273:1998;5858-5868.
74. Roth S.Y., Denu J.M., Allis C.D. Histone acetyltransferases. Annu. Rev. Biochem. 70:2001;81-120.
75. Rydberg B., Holley W.R., Mian I.S., Chatterjee A. Chromatin conformation in living cells. support for a zig-zag model of the 30 nm chromatin fiber J. Mol. Biol. 284:1998;71-84.
76. Schnitzler G.R., Cheung C.L., Hafner J.H., Saurin A.J., Kingston R.E., Lieber C.M. Direct imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips. Mol. Cell. Biol. 21:2001;8504-8511.
77. Shen X., Xiao H., Ranallo R., Wu W.H., Wu C. Modulation of ATP-dependent chromatin-remodeling complexes by inositol polyphosphates. Science. 299:2003;112-114.
78. Shiio Y., Eisenman R.N. Histone sumoylation is associated with transcriptional repression. Proc. Natl. Acad. Sci. USA. 100:2003;13225-13230.
79. Simpson R.T. Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry. 17:1978;5524-5531.
80. Smith C.L., Horowitz-Scherer R., Flanagan J.F., Woodcock C.L., Peterson C.L. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat. Struct. Biol. 10:2003;141-145.
81. Sprangers R., Groves M.R., Sinning I., Sattler M. High-resolution X-ray and NMR structures of the SMN Tudor domain. conformational variation in the binding site for symmetrically dimethylated arginine residues J. Mol. Biol. 327:2003;507-520.
82. Steger D.J., Haswell E.S., Miller A.L., Wente S.R., O'Shea E.K. Regulation of chromatin remodeling by inositol polyphosphates. Science. 299:2003;114-116.
83. Strahl B.D., Allis C.D. The language of covalent histone modifications. Nature. 403:2000;41-45.
84. Sun Z.W., Allis C.D. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature. 418:2002;104-108.
85. Suto R.K., Clarkson M.J., Tremethick D.J., Luger K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat. Struct. Biol. 7:2000;1121-1124.
86. Swedlow J.R., Hirano T. The making of the mitotic chromosome. modern insights into classical questions Mol. Cell. 11:2003;557-569.
87. Tamaru H., Selker E.U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature. 414:2001;277-283.
88. Thomson S., Mahadevan L.C., Clayton A.L. MAP kinase-mediated signalling to nucleosomes and immediate-early gene induction. Semin. Cell Dev. Biol. 10:1999;205-214.
89. van Holde, K.E. ed. (1988). Chromatin (New York, Springer-Verlag).
90. Wang H., Huang Z.Q., Xia L., Feng Q., Erdjument-Bromage H., Strahl B.D., Briggs S.D., Allis C.D., Wong J., Tempst P., Zhang Y. Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science. 293:2001;853-857.
91. Woodcock C.L., Dimitrov S. Higher-order structure of chromatin and chromosomes. Curr. Opin. Genet. Dev. 11:2001;130-135.
92. Zhang Y. Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev. 17:2003;2733-2740.
93. Zhang Y., Reinberg D. Transcription regulation by histone methylation. interplay between different covalent modifications of the core histone tails Genes Dev. 15:2001;2343-2360.
94. Zhang X., Cheng X. Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides. Structure (Camb). 11:2003;509-520.
95. Zhang K., Tang H., Huang L., Blankenship J.W., Jones P.R., Xiang F., Yau P.M., Burlingame A.L. Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry. Anal. Biochem. 306:2002;259-269.
96. Zhang X., Yang Z., Khan S.I., Horton J.R., Tamaru H., Selker E.U., Cheng X. Structural basis for the product specificity of histone lysine methyltransferases. Mol. Cell. 12:2003;177-185.
97. Zhao K., Chai X., Marmorstein R. Structure of the yeast Hst2 protein deacetylase in ternary complex with 2′-O-acetyl ADP ribose and histone peptide. Structure (Camb). 11:2003;1403-1411.
98. Zhou Y.B., Gerchman S.E., Ramakrishnan V., Travers A., Muyldermans S. Position and orientation of the globular domain of linker histone H5 on the nucleosome. Nature. 395:1998;402-405.