Histone acetylation: Influence on transcription, nucleosome mobility and positioning, and linker histone-dependent transcriptional repression

EMBO Journal

Volumn 16, Issue 8, 1997, Pages 2096-2107

  Ura, Kiyoe ^a,b   Kurumizaka, Hitoshi ^a   Dimitrov, Stefan ^a,c   Almouzni, Geneviève ^a,d   Wolffe, Alan P ^a  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b KURUME UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^c INSTITUT ALBERT BONNIOT   (France)

^d INSTITUT CURIE   (France)

Author keywords

Acetylation; Histones; Nucleosome mobility; Nucleosome positioning; Transcriptional regulation

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; HISTONE;

ACETYLATION; ANIMAL CELL; ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA REPLICATION; DNA SEQUENCE; DNA TEMPLATE; GENE REPRESSION; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA BINDING; TRANSCRIPTION REGULATION; XENOPUS;

ACETYLATION; ACETYLTRANSFERASES; ANIMALS; CELL EXTRACTS; CHROMATIN; DNA REPLICATION; GENE EXPRESSION REGULATION; HELA CELLS; HISTONE ACETYLTRANSFERASES; HISTONES; HUMANS; NUCLEOSOMES; OOCYTES; RNA POLYMERASE III; RNA, RIBOSOMAL, 5S; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC; XENOPUS LAEVIS;

ANIMALIA;

EID: 0030998534     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.8.2096     Document Type: Article

References (108)

1. Allan, J., Harborne, N., Rau, D.C. and Gould, H. (1982) Participation of the core histone 'tails' in the stabilization of the chromatin solenoid. J. Cell Biol., 93, 285-297.
2. Allegra, P., Sterner, R., Clayton, D.F. and Allfrey, V.G. (1987) Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences. J. Mol. Biol., 196, 379-388.
3. Allfrey, V., Faulkner, R.M. and Mirsky, A.E. (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. USA, 51, 786-794.
4. Almouzni, G. and Méchali, M. (1988a) Assembly of spaced chromatin promoted by DNA synthesis in extracts from Xenopus eggs. EMBO J., 7, 664-672.
5. Almouzni, G. and Méchali, M. (1988b) Assembly of spaced chromatin: involvement of ATP and DNA topoisomerase activity. EMBO J., 7, 4355-4365.
6. Almouzni, G., Clark, D.J., Méchali, M. and Wolffe, A.P. (1990a) Chromatin assembly on replicating DNA in vitro. Nucleic Acids Res., 18, 5767-5774.
7. Almouzni, G., Méchali, M. and Wolffe, A.P. (1990b) Competition between transcription complex assembly and chromatin assembly on replicating DNA. EMBO J., 9, 573-582.
8. Almouzni, G., Méchali, M. and Wolffe, A.P. (1991) Transcription complex disruption caused by a transition in chromatin structure. Mol. Cell. Biol., 11, 655-665.
9. Annunziato, A.T. and Seale, R.L. (1983) Histone deacetylation is required for the maturation of newly replicated chromatin. J. Biol. Chem., 258, 12675-12684.
10. Ausio, J. and van Holde, K.E. (1986) Histone hyperacetylation: its effects on nucleosome conformation and stability. Biochemistry, 25, 1421-1428.
11. Barlev, N.A., Candau, R., Wang, L., Darpino, P., Silverman, N. and Berger, S.L. (1995) Characterization of physical interactions of the putative transcriptional adaptor ADA2 with acidic activation domains and TATA-binding-protein. J. Biol. Chem., 270, 19337-19334.
12. Bartsch, J., Truss, M., Bode, J. and Beato, M. (1996) Moderate increase in histone acetylation activates the mouse mammary tumor virus promoter and remodels its nucleosome structure. Proc. Natl Acad. Sci. USA, 93, 10741-10745.
13. Bauer, W.R., Hayes, J.J., White, J.H. and Wolffe, A.P. (1994) Nucleosome structural changes due to acetylation. J. Mol. Chem., 236, 685-690.
14. Becker, P.B. (1994) The establishment of active promoters in chromatin. BioEssays, 16, 541-547.
15. Birkenmeier, E.H., Brown, D.D. and Jordan, E. (1978) A nuclear extract of Xenopus laevis oocytes that accurately transcribes 5S RNA genes. Cell, 15, 1077-1086.
16. Bogenhagen, D.F., Wormington, W.M., and Brown, D.D. (1982) Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state. Cell, 28, 413-121.
17. Braunstein, M., Rose, A.B., Holmes, S.G., Allis, C.D. and Broach, J.R. (1993) Transcriptional silencing in yeast is associated with reduced histone acetylation. Genes Dev., 7, 592-604.
18. Bresnick, E.H., Bustin, M., Marsaud, V., Richard-Foy, H. and Hager, G.L. (1992) The transcriptionally-active MMTV promoter is depleted of H1. Nucleic Acids Res., 20, 373-378.
19. Brownell, J.E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D.G., Roth, S.Y. and Allis, C.D. (1996) Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell, 84, 843-851.
20. Cary, P.D., Crane-Robinson, C., Bradbury, E.M. and Dixon, G.H. (1982) Effect of acetylation on the binding of N-terminal peptides of histone H4 to DNA. Eur. J. Biochem., 127, 137-143.
21. Chen, H., Li, B. and Workman, J.L. (1994) A histone-binding protein nucleoplasmin stimulates transcription factor binding to nucleosomes and factor-induced nucleosome disassembly. EMBO J., 13, 380-390.
22. Chen, T.A. and Allfrey, V.G. (1987) Rapid and reversible changes in nucleosome structure accompany the activation, repression and super induction of the murine proto-oncogenes c-fos and c-myc. Proc. Natl Acad. Sci. USA, 84, 5252-5256.
23. Chen, T.A., Sterner, R., Cozzolino, A. and Allfrey, V.G. (1990) Reversible and irreversible changes in nucleosome structure along the c-fos and c-myc oncogenes following inhibition of transcription. J. Mol. Biol. 212, 481-493.
24. Dasso, M., Dimitrov, S. and Wolffe, A.P. (1994) Nuclear assembly is independent of linker histones. Proc. Natl Acad. Sci. USA, 91, 12477-12481.
25. Dimitrov, S., Almouzni, G., Dasso, M. and Wolffe, A.P. (1993) Chromatin transitions during early Xenopus embryogenesis: changes in histone H4 acetylation and in linker histone type. Dev. Biol., 160, 214-227.
26. Dimitrov, S., Dasso, M.C. and Wolffe, A.P. (1994) Remodeling sperm chromatin in Xenopus laevis egg extracts: the role of core histone phosphorylation and linker histone B4 in chromatin assembly. J. Cell Biol., 126, 591-601.
27. Durrin, L.K., Mann, R.K., Kayne, P.S. and Grunstein, M. (1991) Yeast histone H4 N-terminal sequence is required for promoter activation in vivo. Cell, 65, 1023-1031.
28. Felsenfeld, G. (1992) Chromatin: an essential part of the transcriptional apparatus. Nature, 355, 219-224.
29. Fisher-Adams, G. and Grunstein, M. (1995) Yeast histone H4 and H3 N-termini have different effects on the chromatin structure of the Gal1 promoter. EMBO J., 14, 1468-1477.
30. Garcia-Ramirez, M., Dong, F. and Ausio, J. (1992) Role of the histone 'tails' in the folding of oligonucleosomes depleted of histone H1. J. Biol. Chem., 267, 19587-19595.
31. Garcia-Ramirez, M., Rocchini, C. and Ausio, J. (1995) Modulation of chromatin folding by histone acetylation. J. Biol. Chem., 270, 17923-17928.
32. Godde, J.S., Nakatani, Y. and Wolffe, A.P. (1995) The amino-terminal tails of the core histones and the translational position of the TATA box determine TBP/TFIIA association with nucleosomal DNA. Nucleic Acids Res., 23, 4557-4564.
33. Grunstein, M., Durrin, L.K., Mann, R.K., Fisher-Adams, G. and Johnson, L.M. (1992) Histones: regulators of transcription in yeast. In McKnight, S. and Yamamoto, K. (eds). Transcriptional Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 1295-1315.
34. Hansen, J.C. and Wolffe, A.P. (1992) Chromatin folding inhibits both transcription initiation and elongation by RNA polymerase III. Biochemistry, 31, 7977-7988.
35. Hayes, J.J. and Wolffe, A.P. (1992a) The interaction of transcription factors with nucleosomal DNA. BioEssays, 14, 597-603.
36. Hayes, J.J. and Wolffe, A.P. (1992b) Histones H2A/H2B inhibit the interactions of transcription factor IIIA with the Xenopus borealis somatic 5S RNA gene in a nucleosome. Proc. Natl Acad. Sci. USA, 89, 1229-1233.
37. Hayes, J.J. and Wolffe, A.P. (1993) Preferential and asymmetric interaction of linker histones with 5S DNA in the nucleosome. Proc. Natl Acad. Sci. USA, 90, 6415-6419.
38. Hayes, J.J., Kaplan, R., Ura, K., Pruss, D. and Wolffe, A.P. (1996) Basic residues within a putative DNA-binding surface in the globular domain of linker histones are not essential for specific binding to the nucleosome core. J. Biol. Chem., 271, 25817-25822.
39. Hebbes, T.R., Thorne, A.W. and Crane-Robinson, C. (1988) A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J., 7, 1395-1402.
40. Hebbes, T.R., Thorne, A.W., Clayton, A.L. and Crane-Robinson, C. (1992) Histone acetylation and globin gene switching. Nucleic Acids Res., 20, 1017-1022.
41. Hebbes, T.R., Clayton, A.L., Thorne, A.W. and Crane-Robinson, C. (1994) Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken β-globin chromosomal domain. EMBO J., 13, 1823-1830.
42. Hong, L., Schroth, G.P., Matthews, H.R., Yau, P. and Bradbury, E.M. (1993) Studies of the DNA binding properties of the histone H4 amino terminus. J. Biol. Chem., 268, 305-314.
43. Imbalzano, A.M., Kwon, H., Green, M.R. and Kingston, R.E. (1994) Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature, 370, 481-485.
44. Jackson, V., Shires, A., Tanphaichitr, N. and Chalkley, R. (1976) Modification of histones immediately after synthesis. J. Mol. Biol., 104, 471-483.
45. Juan, L.J., Utley, R., Adams, C.C., Vettese-Dadey, M. and Workman, J.L. (1994) Differential repression of transcription factor binding by histone H1 is regulated by the core histone amino termini. EMBO J., 13, 6031-6040.
46. Kamakaka, R.T. and Thomas, J.O. (1990) Chromatin structure of transcriptionally competent and repressed genes. EMBO J., 9, 3997-4006.
47. Kayne, P.S., Kim, U.J., Han, M., Mullen, J.R., Yoshizaki, F. and Grunstein, M. (1988) Extremely conserved histone H4 N-terminus is dispensible for growth but essential for repressing the silent mating loci in yeast. Cell, 55, 27-39.
48. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227, 680-685.
49. Lee, D.Y., Hayes, J.J., Pruss, D. and Wolffe, A.P. (1993) A positive role for histone acetylation in transcription factor binding to nucleosomal DNA. Cell, 72, 73-84.
50. Lorch, Y., La Pointe, J.W. and Kornberg, R.D. (1987) Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell, 49, 203-210.
51. Meersseman, G., Pennings, S. and Bradbury, E.M. (1991) Chromatosome positioning on assembled long chromatin: linker histones affect nucleosome placement on 5S DNA. J. Mol. Biol., 220, 89-100.
52. Meersseman, G., Pennings, S. and Bradbury, E.M. (1992) Mobile nucleosomes - a general behavior. EMBO J., 11, 2951-2959.
53. II250 subunit of TFIID has histone acetyltransferase activity. Cell, 87, 1261-1270.
54. Nightingale, K., Dimitrov, S., Reeves, R. and Wolffe, A.P. (1996a) Evidence for a shared structural role for HMG1 and linker histones B4 and H1 in organizing chromatin. EMBO J., 15, 548-561.
55. Nightingale, K.P., Pruss, D. and Wolffe, A.P. (1996) A single high affinity binding site for histone H1 in a nucleosome containing the Xenopus borealis 5S ribosomal RNA gene. J. Biol Chem., 271, 7090-7094.
56. Norton, V.G., Imai, B.S., Yau, P. and Bradbury, E.M. (1989) Histone acetylation reduces nucleosome core particle linking number change. Cell, 57, 449-457.
57. Norton, V.G., Marvin, K.W., Yau, P. and Bradbury, E.M. (1990) Nucleosome linking number change controlled by acetylation of histones H3 and H4. J. Biol. Chem., 265, 19848-19852.
58. O'Neill, L.P. and Turner, B.M. (1995) Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner. EMBO J., 14, 3946-3957.
59. Ogryzko, V.V., Schiltz, R.L., Russanova, V., Howard, B.H. and Nakatani, Y. (1996) The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell, 87, 953-959.
60. Oliva, R., Bazett-Jones, D.P., Locklear, L. and Dixon, G.H. (1990) Histone hyperacetylation can induce unfolding of the nucleosome core particle. Nucleic Acids Res., 18, 2739-2747.
61. Owen-Hughes, T. and Workman, J.L. (1994) Experimental analysis of chromatin function in transcriptional control. Crit. Rev. Euk. Gene Expr., 4, 1-39.
62. Panyim, S. and Chalkley, R. (1969) The heterogeneity of histone I. A quantative analysis of calf histones in very long polyacrylamide gels. Biochemistry, 8, 3972-3979.
63. Parthun, M.R., Widom, J. and Gottschling, D.E. (1996) The major cytoplasmic histone acetyltransferase in yeast: links to chromatin replication and histone metabolism. Cell, 87, 85-94.
64. Pennings, S., Meersseman, G. and Bradbury, E.M. (1994) Linker histones H1 and H5 prevent the mobility of positioned nucleosomes. Proc. Natl Acad. Sci. USA, 91, 10275-10279.
65. Perlmann, T. and Wrange, O. (1988) Specific glucocorticoid receptor binding to DNA reconstituted in a nucleosome. EMBO J., 7, 3073-3083.
66. Perry, C.A. and Annunziato, A.T. (1989) Influence of histone acetylation on the solubility, H1 content and DNase I sensitivity of newly replicated chromatin. Nucleic Acids Res., 17, 4275-4291.
67. Perry, C.A. and Annunziato, A.T. (1991) Histone acetylation reduces H1-mediated nucleosome interactions during chromatin assembly. Exp. Cell. Res., 196, 337-345.
68. Ridsdale, J.A., Henzdel, M.F., Decluve, G.P. and Davie, J.R. (1990) Histone acetylation alters the capacity of the H1 histones to condense transcriptionally active/competent chromatin. J. Biol. Chem., 265, 5150-5156.
69. Ruiz-Carrillo, A., Wangh, L.J. and Allfrey, V.G. (1975) Processing of newly synthesized histone molecules. Science, 190, 117-128.
70. Russanova, V., Venkov, C. and Tsanev, R. (1980) A comparison of histone variants in different rat tissues. Cell Differ., 9, 339-350.
71. Russanova, V., Stephanova, E., Pashev, I. and Tsanev, R. (1989) Histone variants in mouse centromeric chromatin. Mol. Cell. Biochem., 90, 1-7.
72. Schild, C., Claret, F.-X., Wahli, W. and Wolffe, A.P. (1993) A nucleosome-dependent static loop potentiates estrogen-regulated transcription from the Xenopus vitellogenin B1 promoter in vitro. EMBO J., 12, 423-433.
73. Shen, X. and Gorovsky, M.A. (1996) Linker histone H1 regulates specific gene expression but not global transcription in vivo. Cell, 86, 475-483.
74. Shimamura, A. and Worcel, A. (1989) The assembly of regularly spaced nucleosomes in the Xenopus oocyte S150 extract is accompanied by deacetylation of histone H4. J. Biol. Chem., 264, 14524-14530.
75. Simpson, R.T. (1991) Nucleosome positioning: occurrence, mechanisms and functional consequences. Progr. Nucleic Acids Mol. Biol., 40, 143-184.
76. Sobel, R.E., Cook, R.G., Perry, C.A., Annunziato, A.T. and Allis, C.D. (1995) Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4. Proc. Natl Acad. Sci. USA, 92, 1237-1241.
77. Svaren, J. and Horz, W. (1996) Regulation of gene expression by nucleosomes. Curr. Opin. Genet. Dev., 6, 164-170.
78. Svaren, J. and Horz, W. (1995) Interplay between nucleosomes and transcription factors at the yeast PHO5 promoter. Semin. Cell Biol., 6, 177-183.
79. Tatchell, K. and van Holde, K.E. (1977) Reconstitution of chromatin core particles. Biochemistry, 16, 5295-5303.
80. Tazi, J. and Bird, A. (1990) Alternative chromatin structure at CpG islands. Cell, 60, 902-920.
81. Thoma, F., Koller, T. and 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, 403-427.
82. Thomas, J.O. (1984) The higher order structure of chromatin and histone H1. J. Cell Sci. Suppl., 1, 1-20.
83. Truss, M., Bartsch, J., Schelbert, A., Haché, R.J.G. and Beato, M. (1995) Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo. EMBO J., 14, 1737-1751.
84. Turner, B.M. (1991). Histone acetylation and control of gene expression. J. Cell Sci., 99, 13-20.
85. Turner, B.M. (1993) Decoding the nucleosome. Cell, 75, 5-8.
86. Turner, B. and Fellows, G. (1989) Specific antibodies reveal ordered and cell cycle-related use of histone H4 acetylation sites in mammalian cells. Eur. J. Biochem., 179, 131-139.
87. Turner, B.M. and O'Neill, L.P. (1995) Histone acetylation in chromatin and chromosomes. Semin. Cell Biol., 6, 229-236.
88. Turner, B.M., Birley, A.J. and Lavender, J. (1992) Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell, 69, 375-384.
89. Ura, K., Wolffe, A.P. and Hayes, J.J. (1994) Core histone acetylation does not block linker histone binding to a nucleosome including a Xenopus borealis 5S rRNA gene. J. Biol. Chem., 269, 27171-27174.
90. Ura, K., Hayes, J.J. and Wolffe, A.P. (1995) A positive role for nucleosome mobility in the transcriptional activity of chromatin templates: restriction by linker histones. EMBO J., 14, 3752-3765.
91. Ura, K., Nightingale, K. and Wolffe, A.P. (1996) Differential association of HMG1 and linker histones B4 and H1 with dinucleosomal DNA: structural transitions and transcriptional repression. EMBO J., 15, 4959-4969.
92. Varga-Weisz, P.D., Blank, T.A. and Becker, P.B. (1995) Energy-dependent chromatin accessibility and nucleosome mobility in a cell free system. EMBO J., 14, 2209-2216.
93. Verreault, A., Kaufman, P.D., Kobayashi, R. and Stillman, B. (1996) Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell, 87, 95-104.
94. Vettese-Dadey, M., Walter, P., Chen, H., Juan, L.-J. and Workman, J.L. (1994) Role of the histone amino termini in facilitated binding of a transcription factor, GAL4-AH to nucleosome cores. Mol. Cell. Biol., 14, 970-981.
95. Vettese-Dadey, M., Grant, P.A., Hebbes, R.T., Crane-Robinson, C., Allis, C.D. and Workman, J.L. (1996) Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. EMBO J., 15, 2508-2518.
96. Wallrath, L.L., Lu, Q., Granok, H. and Elgin, S.C.R. (1994) Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. BioEssays, 16, 165-170.
97. West, M.H.P. and Bonner, W.M. (1980) Histone H2B can be modified by the attachment of ubiquitin. Nucleic Acids Res., 8, 4671-4680.
98. Wolffe, A.P. (1989) Dominant and specific repression of Xenopus oocyte 5S RNA genes and satellite I DNA by histone H1. EMBO J., 8, 527-537.
99. Wolffe, A.P. (1995) Chromatin: Structure and Function. 2nd edn. Academic Press, London.
100. Wolffe, A.P. and Pruss, D. (1996) Targeting chromatin disruption: transcription factors that acetylate histones. Cell, 84, 817-819.
101. Wolffe, A.P. Jordan, E. and Brown, D.D. (1986) A bacteriophage RNA polymerase transcribes through a Xenopus 5S RNA gene transcription complex without disrupting it. Cell, 44, 381-389.
102. Wolffe, A.P., Andrews, M.T., Crawford, E.T., Losa, R.M. and Brown, D.D. (1987) Negative supercoiling is not required for 5S RNA transcription in vitro. Cell, 49, 301-303.
103. Wong, J., Shi, Y.-B. and Wolffe, A.P. (1995) A role for nucleosome assembly in both silencing and activation of the Xenopus TRβA gene by the thyroid hormone receptor. Genes Dev., 9, 2696-2711.
104. Worcel, A., Han, S. and Wong, M.L. (1978) Assembly of newly replicated chromatin. Cell, 15, 969-977.
105. Wray, W., Boulikas, T., Wray, V. and Hancock, R. (1981) Silver staining of proteins in polyacrylamide gels. Anal. Biochem., 118, 197-203.
106. Yang, X.J., Ogryzko, V.V., Nishikawa, J.H., Howard, B. and Nakatani, Y. (1996) A p300/CBP-associated factor that competes with the adenoviral E1A oncoprotein. Nature, 382, 319-324.
107. Yoshida, M., Horinouoshi, S. and Beppu, T. (1995) Trichostatin A and trapoxin: novel chemical probes for the role of histone acetylation in chromatin structure and function. BioEssays, 17, 423-430.
108. Zweidler, A. (1978) Resolution of histones by polyacrylamide gel electrophoresis in the presence of nonionic detergent. Methods Cell Biol., 17, 223-233.