Role of covalent modifications of histones in regulating gene expression

Gene

Volumn 240, Issue 1, 1999, Pages 1-12

  Spencer, Virginia A ^a   Davie, James R ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

Author keywords

Chromatin structure; Gene expression; Histone acetylation; Methylation; Phosphorylation; Ubiquitination

Indexed keywords

CELL NUCLEUS DNA; DNA DIRECTED RNA POLYMERASE III; HISTONE; HISTONE ACETYLTRANSFERASE; PHOSPHATASE; PROTAMINE KINASE;

ACETYLATION; CHROMATIN; DNA STRUCTURE; ENZYME ACTIVITY; GENE ACTIVATION; GENE EXPRESSION REGULATION; GENE STRUCTURE; GENETIC TRANSCRIPTION; HUMAN; METHYLATION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEIN STRUCTURE; REVIEW;

ACETYLATION; ANIMALS; BINDING SITES; CHROMATIN; GENE EXPRESSION REGULATION; HISTONES; HUMANS; METHYLATION; PHOSPHORYLATION; UBIQUITINS;

EUKARYOTA;

EID: 0032702598     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(99)00405-9     Document Type: Review

References (99)

1. Alberts A.S., Geneste O., Treisman R. Activation of SRF-regulated chromosomal templates by Rho-family GTPases requires a signal that also induces H4 hyperacetylation. Cell. 92:1998;475-487.
2. Annunziato A.T., Eason M.B., Perry C.A. Relationship between methylation and acetylation of arginine-rich histones in cycling and arrested HeLa cells. Biochemistry. 34:1995;2916-2924.
3. Baneres J.L., Martin A., Parello J. The N tails of histones H3 and H4 adopt a highly structured conformation in the nucleosome. J. Mol. Biol. 273:1997;503-508.
4. Barratt M.J., Hazzalin C.A., Cano E., Mahadevan L.C. Mitogen-stimulated phosphorylation of histone H3 is targeted to a small hyperacetylation-sensitive fraction. Proc. Natl. Acad. Sci. USA. 91:1994;4781-4785.
5. Blanco J.C., Minucci S., Lu J., Yang X.J., Walker K.K., Chen H., Evans R.M., Nakatani Y., Ozato K. The histone acetylase PCAF is a nuclear receptor coactivator. Genes Dev. 12:1998;1638-1651.
6. Brady M.E., Ozanne D.M., Gaughan L., Waite I., Cook S., Neal D.E., Robson C.N. Tip60 is a nuclear hormone receptor coactivator. J. Biol. Chem. 274:1999;17599-17604.
7. Braunstein M., Rose A.B., Holmes S.G., Allis C.D., Broach J.R. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev. 7:1993;592-604.
8. Braunstein M., Sobel R.E., Allis C.D., Turner B.M., Broach J.R. Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol. Cell. Biol. 16:1996;4349-4356.
9. Chadee D.N., Hendzel M.J., Tylipski C.P., Allis C.D., Bazett-Jones D.P., Wright J.A., Davie J.R. Increased ser-10 phosphorylation of histone H3 in mitogen- stimulated and oncogene-transformed mouse fibroblasts. J. Biol. Chem. 274:1999;24914-24920.
10. Coffee B., Zhang F., Warren S.T., Reines D. Acetylated histones are associated with FMR1 in normal but not fragile X-syndrome cells. Nat. Genet. 22:1999;98-101.
11. Davie J.R. Nuclear matrix, dynamic histone acetylation and transcriptionally active chromatin. Mol. Biol. Rep. 24:1997;197-207.
12. Davie J.R., Chadee D.N. Regulation and regulatory parameters of histone modifications. J. Cell. Biochem. 30:(31):1998;203-213.
13. Davie J.R., Murphy L.C. Level of ubiquitinated histone H2B in chromatin is coupled to ongoing transcription. Biochemistry. 29:1990;4752-4757.
14. DeManno D.A., Cottom J.E., Kline M.P., Peters C.A., Maizels E.T., Hunzicker-Dunn M. Follicle-stimulating hormone promotes histone H3 phosphorylation on serine-10. Mol. Endocrinol. 13:1999;91-105.
15. Edmondson D.G., Smith M.M., Roth S.Y. Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev. 10:1996;1247-1259.
16. Feng J., Villeponteau B. High-resolution analysis of c-fos chromatin accessibility using a novel DNase I-PCR assay. Biochim. Biophys. Acta. 1130:1992;253-258.
17. Fischle W., Emiliani S., Hendzel M.J., Nagase T., Nomura N., Voelter W., Verdin E. A new family of human histone deacetylases related to Saccharomyces cerevisiae HDA1p. J. Biol. Chem. 274:1999;11713-11720.
18. Fisher A.L., Caudy M. Groucho proteins: transcriptional corepressors for specific subsets of DNA-binding transcription factors in vertebrates and invertebrates. Genes Dev. 12:1998;1931-1940.
19. Fisher-Adams G., Grunstein M. Yeast histone H4 and H3 N-termini have different effects on the chromatin structure of the GAL1 promoter. EMBO J. 14:1995;1468-1477.
20. Fletcher T.M., Hansen J.C. The nucleosomal array: structure/function relationships. Crit. Rev. Eukaryotic Gene Expr. 6:1996;149-188.
21. Garcia-Ramirez M., Rocchini C., Ausio J. Modulation of chromatin folding by histone acetylation. J. Biol. Chem. 270:1995;17923-17928.
22. Grant P.A., Eberharter A., John S., Cook R.G., Turner B.M., Workman J.L. Expanded lysine acetylation specificity of Gcn5 in native complexes. J. Biol. Chem. 274:1999;5895-5900.
23. Grant P.A., Schieltz D., Pray-Grant M.G., Steger D.J., Reese J.C., Yates 3 J.R., Workman J.L. A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell. 94:1998;45-53.
24. Grant P.A., Schieltz D., Pray-Grant M.G., Yates 3 J.R., Workman J.L. The ATM-related cofactor Tra1 is a component of the purified SAGA complex. Mol. Cell. 2:1998;863-867.
25. Grozinger C.M., Hassig C.A., Schreiber S.L. Three proteins define a class of human histone deacetylases related to yeast Hda1p. Proc. Natl. Acad. Sci. USA. 96:1999;4868-4873.
26. Grunstein M. Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell. 93:1998;325-328.
27. Hamamori Y., Sartorelli V., Ogryzko V., Puri P.L., Wu H.Y., Wang J.Y., Nakatani Y., Kedes L. Regulation of histone acetyltransferases p300 and PCAF by the bHLH protein twist and adenoviral oncoprotein E1A. Cell. 96:1999;405-413.
28. Hansen J.C., Tse C., Wolffe A.P. Structure and function of the core histone N-termini: more than meets the eye. Biochemistry. 37:1998;17637-17641.
29. Hebbes T.R., Clayton A.L., Thorne A.W., Crane-Robinson C. Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken b-globin chromosomal domain. EMBO J. 13:1994;1823-1830.
30. Hendzel M.J., Davie J.R. Distribution of methylated histones and histone methyltransferases in chicken erythrocyte chromatin. J. Biol. Chem. 264:1989;19208-19214.
31. Hendzel M.J., Davie J.R. Dynamically acetylated histones of chicken erythrocytes are selectively methylated. Biochem. J. 273:1991;753-758.
32. Herrera J.E., Sakaguchi K., Bergel M., Trieschmann L., Nakatani Y., Bustin M. Specific acetylation of chromosomal protein HMG-17 by PCAF alters its interaction with nucleosomes. Mol. Cell Biol. 19:1999;3466-3473.
33. Howe L., Ranalli T.A., Allis C.D., Ausio J. Transcriptionally active Xenopus laevis somatic 5 S ribosomal RNA genes are packaged with hyperacetylated histone H4, whereas transcriptionally silent oocyte genes are not. J. Biol. Chem. 273:1998;20693-20696.
34. Hung H.L., Lau J., Kim A.Y., Weiss M.J., Blobel G.A. CREB-Binding protein acetylates hematopoietic transcription factor GATA-1 at functionally important sites. Mol. Cell Biol. 19:1999;3496-3505.
35. Ikeda K., Steger D.J., Eberharter A., Workman J.L. Activation domain-specific and general transcription stimulation by native histone acetyltransferase complexes. Mol. Cell Biol. 19:1999;855-863.
36. Jin S., Scotto K.W. Transcriptional regulation of the MDR1 gene by histone acetyltransferase and deacetylase Is mediated by NF-Y. Mol. Cell Biol. 18:1998;4377-4384.
37. Kadosh D., Struhl K. Targeted recruitment of the Sin3-rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell Biol. 18:1998;5121-5127.
38. Kim T.K., Kim T.H., Maniatis T. Efficient recruitment of TFIIB and CBP-RNA polymerase II holoenzyme by an interferon-beta enhanceosome in vitro. Proc. Natl. Acad. Sci. USA. 95:1998;12191-12196.
39. Kimura A., Horikoshi M. Tip60 acetylates six lysines of a specific class in core histones in vitro. Genes Cells. 3:1998;789-800.
40. Koipally J., Renold A., Kim J., Georgopoulos K. Repression by Ikaros and Aiolos is mediated through histone deacetylase complexes. EMBO J. 18:1999;3090-3100.
41. Kouzarides T. Histone acetylases and deacetylases in cell proliferation. Curr. Opin. Genet. Dev. 9:1999;40-48.
42. Krajewski W.A., Becker P.B. Reconstitution of hyperacetylated, DNase I-sensitive chromatin characterized by high conformational flexibility of nucleosomal DNA. Proc. Natl. Acad. Sci. USA. 95:1998;1540-1545.
43. Kraus W.L., Kadonaga J.T. p300 and estrogen receptor cooperatively activate transcription via differential enhancement of initiation and reinitiation. Genes Dev. 12:1998;331-342.
44. Krebs J.E., Kuo M.H., Allis C.D., Peterson C.L. Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. Genes Dev. 13:1999;1412-1421.
45. Kuo M.H., Zhou J., Jambeck P., Churchill M.E., Allis C.D. Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev. 12:1998;627-639.
46. Lee H.L., Archer T.K. Prolonged glucocorticoid exposure dephosphorylates histone H1 and inactivates the MMTV promoter. EMBO J. 17:1998;1454-1466.
47. Lenfant F., Mann R.K., Thomsen B., Ling X., Grunstein M. All four core histone N-termini contain sequences required for the repression of basal transcription in yeast. EMBO J. 15:1996;3974-3985.
48. Leuba S.H., Walia H.S., Van Holde K., Zlatanova J., Davie J.R., Bustamante C. Chromatin fibers associated with acetylated and ubiquitinated histones adopt a more extended structure than bulk soluble chromatin: evidence from scanning force microscopy. J. Biomol. Struct. Dynam. 12:1995;A140.
49. Liu L., Scolnick D.M., Trievel R.C., Zhang H.B., Marmorstein R., Halazonetis T.D., Berger S.L. p53 sites acetylated In vitro by PCAF and p300 are acetylated in vivo in response to DNA damage. Mol. Cell Biol. 19:1999;1202-1209.
50. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
51. Luo R.X., Postigo A.A., Dean D.C. Rb interacts with histone deacetylase to repress transcription. Cell. 92:1998;463-473.
52. Madisen L., Krumm A., Hebbes T.R., Groudine M. The immunoglobulin heavy chain locus control region increases histone acetylation along linked c-myc genes. Mol. Cell Biol. 18:1998;6281-6292.
53. Mahadevan L.C., Willis A.C., Barratt M.J. Rapid histone H3 phosphorylation in response to growth factors, phorbol esters, okadaic acid, and protein synthesis inhibitors. Cell. 65:1991;775-783.
54. Martinez-Balbas M.A., Bannister A.J., Martin K., Haus-Seuffert P., Meisterernst M., Kouzarides T. The acetyltransferase activity of CBP stimulates transcription. EMBO J. 17:1998;2886-2893.
55. Merika M., Williams A.J., Chen G., Collins T., Thanos D. Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription. Mol. Cell. 1:1998;277-287.
56. Moore S.C., Ausio J. Major role of the histones H3-H4 in the folding of the chromatin fiber. Biochem. Biophys. Res. Commun. 230:1997;136-139.
57. Munshi N., Merika M., Yie J., Senger K., Chen G., Thanos D. Acetylation of HMG I(Y) by CBP turns off IFN beta expression by disrupting the enhanceosome. Mol. Cell. 2:1998;457-467.
58. Muscat G.E., Burke L.J., Downes M. The corepressor N-CoR and its variants RIP13a and RIP13Delta1 directly interact with the basal transcription factors TFIIB, TAFII32 and TAFII70. Nucleic Acids Res. 26:1998;2899-2907.
59. Mutskov V., Gerber D., Angelov D., Ausio J., Workman J., Dimitrov S. Persistent interactions of core histone tails with nucleosomal DNA following acetylation and transcription factor binding. Mol. Cell Biol. 18:1998;6293-6304.
60. Ngg H.H., Bird A. DNA methylation and chromatin modification. Curr. Opin. Genet. Dev. 9:1999;158-163.
61. Nightingale K.P., Wellinger R.E., Sogo J.M., Becker P.B. Histone acetylation facilitates RNA polymerase II transcription of the Drosophila hsp26 gene in chromatin. EMBO J. 17:1998;2865-2876.
62. Nomura T., Khan M.M., Kaul S.C., Dong H.D., Wadhwa R., Colmenares C., Kohno I., Ishii S. Ski is a component of the histone deacetylase complex required for transcriptional repression by mad and thyroid hormone receptor. Genes Dev. 13:1999;412-423.
63. Ogryzko V.V., Kotani T., Zhang X., Schlitz R.L., Howard T., Yang X.J., Howard B.H., Qin J., Nakatani Y. Histone-like TAFs within the PCAF histone acetylase complex. Cell. 94:1998;35-44.
64. Ohba R., Steger D.J., Brownell J.E., Mizzen C.A., Cook R.G., Cote J., Workman J.L., Allis C.D. A novel H2A/H4 nucleosomal histone acetyltransferase in Tetrahymena thermophila. Mol. Cell Biol. 19:1999;2061-2068.
65. O'Neill L.P., Turner B.M. Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner. EMBO J. 14:1995;3946-3957.
66. Palaparti A., Baratz A., Stifani S. The Groucho/transducin-like enhancer of split transcriptional repressors interact with the genetically defined amino-terminal silencing domain of histone H3. J. Biol. Chem. 272:1997;26604-26610.
67. Parekh B.S., Maniatis T. Virus infection leads to localized hyperacetylation of histones H3 and H4 at the IFN-beta promoter. Mol. Cell. 3:1999;125-129.
68. Parkhurst S.M. Groucho: making its Marx as a transcriptional co-repressor. Trends Genet. 14:1998;130-132.
69. Pinaud S., Mirkovitch J. Regulation of c-fos expression by RNA polymerase elongation competence. J. Mol. Biol. 280:1998;785-798.
70. Puig O.M., Belles E., Lopez-Rodas G., Sendra R., Tordera V. Interaction between N-terminal domain of H4 and DNA is regulated by the acetylation degree. Biochim. Biophys. Acta. 1397:1998;79-90.
71. Ridsdale J.A., Hendzel M.J., Delcuve G.P., Davie J.R. Histone acetylation alters the capacity of the H1 histones to condense transcriptionally active/competent chromatin. J. Biol. Chem. 265:1990;5150-5156.
72. Sakaguchi K., Herrera J.E., Saito S., Miki T., Bustin M., Vassilev A., Anderson C.W., Appella E. DNA damage activates p53 through a phosphorylation-acetylation cascade. Genes Dev. 12:1998;2831-2841.
73. Sathyanarayana U.G., Freeman L.A., Lee M.S., Garrard W.T. RNA polymerase-specific nucleosome disruption by transcription in vivo. J. Biol. Chem. 274:1999;16431-16436.
74. Schiltz R.L., Mizzen C.A., Vassilev A., Cook R.G., Allis C.D., Nakatani Y. Overlapping but distinct patterns of histone acetylation by the human coactivators p300 and PCAF within nucleosomal substrates. J. Biol. Chem. 274:1999;1189-1192.
75. Smith E.R., Belote J.M., Schiltz R.L., Yang X.J., Moore P.A., Berger S.L., Nakatani Y., Allis C.D. Cloning of Drosophila GCN5: conserved features among metazoan GCN5 family members. Nucleic Acids Res. 26:1998;2948-2954.
76. Smith E.R., Eisen A., Gu W., Sattah M., Pannuti A., Zhou J., Cook R.G., Lucchesi J.C., Allis C.D. ESA1 is a histone acetyltransferase that is essential for growth in yeast. Proc. Natl. Acad. Sci. USA. 95:1998;3561-3565.
77. Steger D.J., Eberharter A., John S., Grant P.A., Workman J.L. Purified histone acetyltransferase complexes stimulate HIV-1 transcription from preassembled nucleosomal arrays. Proc. Natl. Acad. Sci. USA. 95:1998;12924-12929.
78. Sun J.-M., Chen H.Y., Moniwa M., Samuel S., Davie J.R. Purification and characterization of chicken erythrocyte histone deacetylase 1. Biochemistry. 38:1999;5939-5947.
79. Tong J.K., Hassig C.A., Schnitzler G.R., Kingston R.E., Schreiber S.L. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature. 395:1998;917-921.
80. Trieschmann L., Martin B., Bustin M. The chromatin unfolding domain of chromosomal protein HMG-14 targets the N-terminal tail of histone H3 in nucleosomes. Proc. Natl. Acad. Sci. USA. 95:1998;5468-5473.
81. Tse C., Hansen J.C. Hybrid trypsinized nucleosomal arrays: identification of multiple functional roles of the H2A/H2B and H3/H4 N-termini in chromatin fiber compaction. Biochemistry. 36:1997;11381-11388.
82. Tse C., Sera T., Wolffe A.P., Hansen J.C. Disruption of higher order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol. Cell. Biol. 18:1998;4629-4638.
83. Turner B.M., O'Neill L.P., Allan I.M. Histone H4 acetylation in human cells. Frequency of acetylation at different sites defined by immunolabeling with site-specific antibodies. FEBS Lett. 253:1989;141-145.
84. Utley R.T., Ikeda K., Grant P.A., Cote J., Steger D.J., Eberharter A., John S., Workman J.L. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature. 394:1998;498-502.
85. Van Holde K.E. Chromatin. 1988;Springer, New York.
86. Vassilev A., Yamauchi J., Kotani T., Prives C., Avantaggiati M.L., Qin J., Nakatani Y. The 400 kDa subunit of the PCAF histone acetylase complex belongs to the ATM superfamily. Mol. Cell. 2:1998;869-875.
87. Verdel A., Khochbin S. Identification of a new family of higher eukaryotic histone deacetylases. Coordinate expression of differentiation-dependent chromatin modifiers. J. Biol. Chem. 274:1999;2440-2445.
88. Wade P.A., Jones P.L., Vermaak D., Wolffe A.P. A multiple subunit Mi-2 histone deacetylase from Xenopus laevis cofractionates with an associated Snf2 superfamily ATPase. Curr. Biol. 8:1998;843-846.
89. Walia H., Chen H.-Y., Sun J.-M., Holth L.T., Davie J.R. Histone acetylation is required to maintain the unfolded nucleosome structure associated with transcribing DNA. J. Biol. Chem. 273:1998;14516-24522.
90. Waring P., Khan T., Sjaarda A. Apoptosis induced by gliotoxin is preceeded by phosphorylation of histone H3 and enhanced sensitivity of chromatin to nuclease digestion. J. Biol. Chem. 272:1997;17929-17936.
91. Waterborg J.H., Robertson A.J., Tatar D.L., Borza C.M., Davie J.R. Histones of Chlamydomonas veinhardtii - synthesis, acetylation, and methylation. Plant Physiol. 109:1995;393-407.
92. Wei Y., Yu L., Bowen J., Gorovsky M.A., Allis C.D. Phosphorylation of histone H3 is required for proper chromosome condensation and segregation. Cell. 97:1999;99-109.
93. Workman J.L., Kingston R.E. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:1998;545-579.
94. Xu W., Edmondson D.G., Roth S.Y. Mammalian GCN5 and P/CAF acetyltransferases have homologous amino-terminal domains important for recognition of nucleosomal substrates. Mol. Cell Biol. 18:1998;5659-5669.
95. Xue Y., Wong J., Moreno G.T., Young M.K., Cote J., Wang W. NURD, a novel complex with both ATP-dependent chromatin- remodeling and histone deacetylase activities. Mol. Cell. 2:1998;851-861.
96. Zhang W., Bieker J.J. Acetylation and modulation of erythroid Krüppel-like factor (EKLF) activity by interaction with histone acetyltransferases. Proc. Natl. Acad. Sci. USA. 95:1998;9855-9860.
97. Zhang Y., LeRoy G., Seelig H.P., Lane W.S., Reinberg D. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell. 95:1998;279-289.
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.
99. Zlatanova J., Leuba S.H., Van Holde K. Chromatin fiber structure: morphology, molecular determinants, structural transitions. Biophys. J. 74:1998;2554-2566.