Role of Histone Deacetylase Complexes in the Regulation of Chromatin Metabolism (original) (raw)

• Aasland R, Gibson TJ, Stewart AF (1995) The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci 20: 56–59
  Article PubMed CAS Google Scholar
• Aasland R (1996) 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: 87–88
  PubMed CAS Google Scholar
• Ayer DE, Lawrence QA, Eisenman RN (1995) Mad-Max transcriptional repression is mediated by ternary complex formation with mammalian homologs of the yeast repressor Sin3. Cell 80: 767–776
  Article PubMed CAS Google Scholar
• Braunstein M, Sobel RE, Allis CD, Turner BM, Broach JR (1996) Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol Cell Biol 16: 4349–4356
  PubMed CAS Google Scholar
• Carmen AA, Rundlett SE, Grunstein M (1996) HDAI and HDA3 are components of a yeast histone deacetylase ( HDA) complex. J Biol Chem 271: 15837–15844
  Google Scholar
• Carmen AA, Griffin PR, Calaycay JR, Rundlett SE, Suka Y. Grunstein M (1999) Yeast HOS3 forms a novel trichostatin A-insensitive homodimer with intrinsic histone deacetylase activity. Proc Natl Acad Sci USA 96: 12356–12361
  Google Scholar
• Cavalli G, Paro R (1998) Chromo-domain proteins: linking chromatin structure to epigenic regulation. Curr Opin Cell Biol 10: 354–360
  Article PubMed CAS Google Scholar
• Corona DF, Langst G, Clapier CR, Bonte EJ, Ferrari S, Tamkun JW, Becker PB (1999) ISWI is an ATP-dependent nucleosome remodelling factor. Mol Cell 3: 239–245
  Article PubMed CAS Google Scholar
• Cowell IG, Austin CA (1997) Self-association of chromo domain peptides. Biochim Biophys Acta 1337: 198–206
  Article PubMed CAS Google Scholar
• DeRubertis F, Kadosh D, Henchoz S, Pauli D, Reuter G, Struhl K, Spierer P (1996) The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature 384: 589–591
  Article CAS Google Scholar
• Eisen JA, Sweder KS, Hanawalt PC (1995) Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res 23: 2715–2723
  Article PubMed CAS Google Scholar
• Ekwall K, Olsson T, Turner BM, Cranston G, Allshire RC (1997) Transient inhibition of histone deacetylation alters the structural and functional imprint at fission yeast centromeres. Cell 91: 1021–1032
  Article PubMed CAS Google Scholar
• Finnin MS, Donigian JR, Cohen A, Richon VM, Rifkind RA, Marks PA, Breslow R, Pavletich NP (1999) Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 401: 188–193
  Article PubMed CAS Google Scholar
• Fischle W, Emiliani S, Hendzel MJ, Nagase T, Nomura N, Voelter W, Verdin E (1999) A new family of human histone deacetylases related to Saccharomyces cerevisiae HDAIp. J Biol Chem 274: 11713–11720
  Article PubMed CAS Google Scholar
• Grewal SI, Bonaduce MJ, Klar Ai (1998) Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast. Genetics 150: 563–576
  PubMed CAS Google Scholar
• Grozinger CM, Hassig CA, Schreiber SL (1999) Three proteins define a class of human histone deacetylases related to yeast Hdalp. Proc Natl Acad Sci USA 96: 4868–4873
  Article PubMed CAS Google Scholar
• Hamiche A, Sandaltzopoulos R, Gdula DA, Wu C (1999) ATP-Dependent Histone Octamer Sliding Mediated by the Chromatin Remodeling Complex NURF. 97: 833–842
  CAS Google Scholar
• Harper SE, Qiu Y, Sharp PA (1996) Sin3 corepressor function in Myc-induced transcription and transformation. Proc Natl Acad Sci USA 93: 8536–8540
  Article PubMed CAS Google Scholar
• Hassig CA, Fleischer TC, Billin AN, Schreiber SL, Ayer DE (1997) Histone deacetylase activity is required for full transcriptional repression by mSin3A. Cell 89: 341–347
  Article PubMed CAS Google Scholar
• Hassig CA, Tong JK, Fleischer TC, Owa T, Grable PG, Ayer DE, Schreiber SL (1998) A role for histone deacetylase activity in HDACI-mediated transcriptional repression 95: 3519–3524
  CAS Google Scholar
• Hendrich B, Bird A (1998) Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol 18: 6538–6547
  PubMed CAS Google Scholar
• Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga JT (1997) ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodelling factor. Cell 90: 145–155
  Article PubMed CAS Google Scholar
• Jeppesen P, Turner BM (1993) The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74: 281–289
  Article PubMed CAS Google Scholar
• Kadosh D, Struhl K (1997) Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89: 365–371
  Article PubMed CAS Google Scholar
• Kadosh D, Struhl K (1998) Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo. Genes Dev 12: 797–805
  Article PubMed CAS Google Scholar
• Kao H-Y, Downes M, Ordentlich P, Evans RM (2000) Isolation of a novel histone deacetylase reveals that class I and class II deacetylases promote SMRT-mediated repression. Genes Dev 14: 55–66
  PubMed CAS Google Scholar
• Kasten MM, Ayer DE, Stillman DJ (1996) SIN3-dependent transcriptional repression by interaction with the Madl DNA binding protein. Mol Cell Biol 16: 4215–4221
  PubMed CAS Google Scholar
• Kasten MM, Dorland S, Stillman DJ (1997) A large protein complex containing the yeast Sin3p and Rpd3p transcriptional regulators. Mol Cell Biol 17: 2852–4858
  Google Scholar
• Kaufman PD, Kobayashi R, Kessler N, Stillman B (1995) The p150 and p60 subunits of chromatin assembly factor l: a molecular link between newly synthesized histones and DNA replication. Cell 81: 1105–1114
  Article PubMed CAS Google Scholar
• Kaufman PD, Kobayashi R, Stillman B (1997) Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-1. Genes Dev 11: 345–357
  Article PubMed CAS Google Scholar
• Kwon H, Imbalzano AN, Khavari PA, Kingston RE, Green MR (1994) Nucleosome disruption and enhancement of activator binding by a human SWI/SNF complex. Nature 370: 477–481
  Article PubMed CAS Google Scholar
• Laherty CD, Yang WM, Sun JM, Davie JR, Seto E, Eisenman RN (1997) Histone deacetylases associated with the mSin3 corepressor mediate Mad transcriptional repression. Cell 89: 349–356
  Article PubMed CAS Google Scholar
• Laherty CD, Billin AN, Lavinsky RM, Yochum GS, Bush AC, Sun JM, Mullen TM, Davie JR, Rose DW, Glass CK, Rosenfeld MG, Ayer DE, Eisenman RN (1998) SAP30, a component of the mSin3 corepressor complex involved in N-CoR-mediated repression by specific transcription factors. Mol Cell 2: 33–42
  Article PubMed CAS Google Scholar
• Längst G, Bonte EJ, Corona DF, Becker PB (1999) Nucleosome Movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. 843–852
  Google Scholar
• Lewis JD, Meehan RR, Henze] WJ, Maureer-Fogy I, Jeppesen P, Klein F, Bird A (1992) Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69: 905–914
  Article PubMed CAS Google Scholar
• Lindt CV, Emiliani S, Verdin E (1996) The expression of a small fraction of cellular genes is changed in response to histone hyperacetylation. Gene Expr 5: 345–253
  Google Scholar
• Luger K, Maumlder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8A resolution. Nature 398: 251–260
  Google Scholar
• Lusser A, Brosch G, Loidl A, Haas H, Loidl P (1997) Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277: 88–91
  Article PubMed CAS Google Scholar
• Ma XJ, Wu J, Altheim BA, Schultz MC, Grunstein M (1998) Deposition-related sites K5/K12 in histone H4 are not required for nucleosome deposition in yeast. Proc Natl Acad Sci USA 95: 6693–6698
  Article PubMed CAS Google Scholar
• Martinez-Balbas MA, Tsukiyama T, Gdula D, Wu C (1998) Drosophila NURF-55, a WD repeat protein involved in histone metabolism. Proc Natl Acad Sci USA 95: 132–137
  Google Scholar
• Meehan RR, Lewis JD, McKay S, Kleiner EL, Bird AP (1989) Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell 58: 499–507
  Article PubMed CAS Google Scholar
• Miska EA, Karlsson C, Langley E, Nielsen SJ, Pines J, Kouzarides T (1999) HDAC4 deacetylase associates with and represses the MEF2 transcription factor. Embo J 18: 5099–5107
  Article PubMed CAS Google Scholar
• Ng HH, Zhang Y, Hendrich B, Johnson CA, Turner BM, Erdjument-Bromage H, Tempst P, Reinberg D, Bird A (1999) MBD2 is a transcriptional repressor belonging to the McCPI histone deacetylase complex. Nat Genet 23: 58–6I
  PubMed CAS Google Scholar
• Paro R, Hogness DS (1991) The Polycomb protein shares a homologous domain with a heterochromatinassociated protein of Drosophila. Proc Nall Acad Sei USA 88: 263–267
  Article CAS Google Scholar
• Parthun MR, Widom J. Gottschling D (1996) The major cytoplasmic histone acetyltransferasein yeast: links to chromatin replication and histone metabolism. Cell 87: 85–94
  Google Scholar
• Qian YW, Lee EY (1995) Dual retinoblastoma-binding proteins with properties related to a negative regulator of Ras in yeast. J Biol Chem 270: 25507–25513
  Article PubMed CAS Google Scholar
• Rundlett SE, Carmen AA, Kobayashi R, Bavykin S, Turner BM, Grunstein M (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci USA 93: 14503–14508
  Article PubMed CAS Google Scholar
• Rundlett SE, Carmen AA, Suka N, Turner BM, Grunstein M (1998) Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone I-14 by RPD3. Nature 392: 831–835
  Article PubMed CAS Google Scholar
• Schreiber-Agus N, Chin L, Chen K, Torres R, Rao G, Guida P, Skoultchi Al, DePinho RA (1995) An amino-terminal domain of Mxi I mediates anti-Myc oncogenic activity and interacts with a homolog of the yeast transcriptional repressor SIN3. Cell 80: 777–786
  Article PubMed CAS Google Scholar
• Seelig HP, Moosbrugger I, Ehrfeld H, Fink T, Renz M, Genth E (1995) The major dermatomyositisspecific Mi-2 autoantigen is a presumed helicase involved in transcriptional activation. Arthritis Rheum 38: 1389–1399
  Article PubMed CAS Google Scholar
• Sherman JM, Pillus L (1997) An uncertain silence. Trends Genet 13: 308–313
  Article PubMed CAS Google Scholar
• Shimamura A, Worcel A (1989) The assembly of regularly spaced nucleosomes in the Xenopus oocyte S-I50 extract is accompanied by deacetylation of histone H4. J Biol Chem 264: 14524–14530
  PubMed CAS Google Scholar
• Smith JS, Boeke JD (1997) An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev 11: 241–254
  Article PubMed CAS Google Scholar
• Smith JS, Brachmann CB, Pillus L, Boeke JD (1998) Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by Sir4p. 149: 1205–1219
  CAS Google Scholar
• Sobel RE, Cook RG. Perry CA, Annunziato AT, Allis CD (1995) Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4. Proc Natl Acad Sei USA 92: 1237–1241
  Article CAS Google Scholar
• Solari F, Bareman A, Ahringcr J (1999) The Caenorhabditis elegans genes eg1–27 and egr-1 are similar to MTA I, a member of a chromatin regulatory complex, and are redundantly required for embryonic patterning. Development 126: 2483–2494
  PubMed CAS Google Scholar
• Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 41–45
  Article PubMed CAS Google Scholar
• Suka N, Carmen AA, Rundlett SE, Grunstein M (1998) The regulation of gene activity by histones and the histone deacetylase RPD3. Cold Spring Harb Symp Quant Biol LXIII: 391–399
  Google Scholar
• Sun ZW, Hampsey M (1999) A general requirement for the Sin3-Rpd3 histone deactylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics 152: 921–932
  PubMed CAS Google Scholar
• Taunton J, Hassig CA, Schreiber SL (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272: 408–411
  Article PubMed CAS Google Scholar
• Thompson JS, Ling X, Grunstein M (1994) Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature 369: 245–247
  Article PubMed CAS Google Scholar
• Thon G, Cohen A, Klar AJ (1994) Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe. Genetics 138: 29–38
  PubMed CAS Google Scholar
• Toh Y, Pencil SD, Nicolson GL (1994) A novel candidate metastasis-associated gene, mtal differentially expressed in highly metastatic mammary adenocarcinoma cell lines. J Biol Chem 269: 22958–22963
  PubMed CAS Google Scholar
• Toh Y, Oki E. Oda S, Tokunaga E, Ohno S, Mehara Y, Nicolson GL, Sugimachi K (1997) Overexpression of the MTAI gene in gastrointestinal carcinomas: correlation with invasion and metastasis. Int J Cancer 74: 459–463
  CAS Google Scholar
• Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL (1998) Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature 395: 917–921
  Article PubMed CAS Google Scholar
• Tsukiyama T. Wu C (1995) Purification and properties of an ATP-dependent nucleosome remodelling factor. Cell 83: 1011–1020
  Google Scholar
• Turner BM, Birley AJ, Lavender 1 (1992) Histone H4 isoforms acetylated at specific lysine residues define
  Google Scholar
• individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell 69:375–384
  Google Scholar
• Tweedie S, Ng HH, Barlow AL, Turner BM, Hendrich B, Bird A (1999) Vestiges of a DNA methylation system in Drosophila melanogasier Nat Genet 23: 389–390
  CAS Google Scholar
• Tyler JK, Bulger M, Kamakaka RT, Kobayashi R, Kadonaga JT (1996) The p55 subunit of Drosophila chromatin assembly factor 1 is homologous to a histone deacetylase associated protein. Mol Cell Biol 16: 6149–6159
  PubMed CAS Google Scholar
• Tyler JK, Adams CR, Chen SR, Kobayashi R, Kamakaka RT, Kadonaga JT (2000) The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402: 555–560
  Article Google Scholar
• Varga-Weisz PD, Wilm M, Bonte E, Dumas K, Mann M, Becker PB (1997) Chromatin remodeling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388: 598–602
  Article PubMed CAS Google Scholar
• Verdel A, Khochbin S (1999) Identification of a new family of higher eukaryotic histone deacetylases. J Biol Chem 274: 2440–2445
  Article PubMed CAS Google Scholar
• Vermaak D, Wade PA, Jones PL, Shi YB, Wolffe AP (1999) Functional analysis of the SINS-histone deacetylase RPD3-RbAp48-histone H4 connection in Xenopus oocyte. Mol Cell Biol 19: 5847–5860
  PubMed CAS Google Scholar
• Verreault A, Kaufman PD, Kobayashi R, Stillman B (1996) Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell 87: 95–104
  Article PubMed CAS Google Scholar
• Verreault A, Kaufman PD, Kobayashi R, Stillman B (1998) Nucleosomal DNA regulates the core-histone binding subunit of the human Hatt acetyltransferase. Curr Biol 8: 96–108
  Article PubMed CAS Google Scholar
• Vidal M, Strich R, Esposito RE, Gaber R (1991a) RPDJ (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Mol Cell Biol 11: 6306–6316
  Google Scholar
• Vidal M (1991b) RPD3 encodes a second factor required to activate maximum positive and negative transcriptional states in Saccharomyces cerevisiae Mol Cell Biol 11:6317–6327
  Google Scholar
• Wade PA, Jones PL, Vermaak D, Wolfe AP (1998) A multiple subunit Mi-2 histone deactylase from Xenopus iaevis cofractionates with an associated Snf2 superfamily ATPase. Curr Biol 8: 843–846
  Article PubMed CAS Google Scholar
• Wade PA, Gegonne A, Jones PL, Ballestar E, Aubry F, Wolffe AP (1999) Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat Genet 23: 62–66
  PubMed CAS Google Scholar
• Wang AH, Bertos NR, Vezmar M, Pelletier N, Crosato M, Heng HH, Th’ng J, Han J, Yang X-J (1999) HDAC4, a human histone deacetylase related to yeast HDA1, is a transcriptional corepressor. Mol Cell Biol 19: 7816–7827
  PubMed CAS Google Scholar
• Woodage T, Basrai MA, Baxevanis AD, Hieter P, Collins FS (1997) Characterization of the CHD family of proteins. Proc Natl Acad Sci USA 94: 11472–11477
  Article PubMed CAS Google Scholar
• Xue Y, Wong J, Moreno GT, Young MK, Cote J, Wang W (1998) NURD, a novel complex with both ATP-dependent chromatin-remodelling and histone deacetylase activities. Mol Cell 2: 851–861
  Article PubMed CAS Google Scholar
• Yang WM, Yao YL, Sun JM, Davie JR, Seto E (1997) Isolation and characterization of cDNAs corresponding to an additional member of the human histone deacetylase gene family. J Biol Chem 272: 28001–28007
  Article PubMed CAS Google Scholar
• Zhang Y, Iratni R, Erdjument-Bromage H, Tempst P, Reinberg D (1997) Histone deacetylases and SAP18, a novel polypeptide, are components of a human Sin3 complex. Cell 89: 357–364
  Article PubMed CAS Google Scholar
• Zhang Y, Sun ZW, Iratni R, Erdjument-Bromage H, Tempst P, Hampsey M, Reinberg D (1998a) SAP30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex. Mol Cell 1: 1021–1031
  Article PubMed CAS Google Scholar
• Zhang Y, LeRoy G, Seelig HP, Lane WS, Reinberg D (1998b) The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodelling activities. Cell 95: 279–289
  Article PubMed CAS Google Scholar
• Zhang Y, Ng HH, Erdjument-Bromage H, Tempst P, Bird A (1999) Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev 13: 1924–1935
  Article PubMed CAS Google Scholar