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PMID: 15494307 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Global position and recruitment of HATs and HDACs in the yeast genome.

Molecular cell ·Vol. 16 ·No. 2 ·2004-10-22 ·Pages 199-209

Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M, Rolfe A, Workman JL, Gifford DK, Young RA

Abstract

Chromatin regulators play fundamental roles in the regulation of gene expression and chromosome maintenance, but the regions of the genome where most of these regulators function has not been established. We explored the genome-wide occupancy of four different chromatin regulators encoded in Saccharomyces cerevisiae. The results reveal that the histone acetyltransferases Gcn5 and Esa1 are both generally recruited to the promoters of active protein-coding genes. In contrast, the histone deacetylases Hst1 and Rpd3 are recruited to specific sets of genes associated with distinct cellular functions. Our results provide new insights into the association of histone acetyltransferases and histone deacetylases with the yeast genome, and together with previous studies, suggest how these chromatin regulators are recruited to specific regions of the genome.

MeSH Terms
Acetyltransferases/metabolism Cell Cycle/genetics,physiology DNA-Binding Proteins/metabolism Genome Histone Acetyltransferases Histone Deacetylases/metabolism NAD/biosynthesis Protein Kinases/metabolism Ribosomal Proteins/genetics,metabolism Saccharomyces cerevisiae/enzymology,genetics,metabolism Saccharomyces cerevisiae Proteins/metabolism Sirtuin 2 Sirtuins/metabolism Spores, Fungal/enzymology,physiology Transcription Factors/metabolism Tryptophan/metabolism
Chemicals
DNA-Binding Proteins Ribosomal Proteins Saccharomyces cerevisiae Proteins Transcription Factors NAD Tryptophan Acetyltransferases Esa1 protein, S cerevisiae GCN5 protein, S cerevisiae Histone Acetyltransferases Protein Kinases HST1 protein, S cerevisiae RPD3 protein, S cerevisiae Sirtuin 2 Sirtuins Histone Deacetylases
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Robert François
Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA. francois.robert@ircm.qc.ca
Pokholok Dmitry K
Hannett Nancy M
Rinaldi Nicola J
Chandy Mark
Rolfe Alex
Workman Jerry L
Gifford David K
Young Richard A
References (86)
86 references, click to expand
  1. Distribution of acetylated histones resulting from Gal4-VP16 recruitment of SAGA and NuA4 complexes.
    EMBO J. 2000 Jun 1;19(11):2629-40 PMID: 10835360
  2. Overlapping roles for the histone acetyltransferase activities of SAGA and elongator in vivo.
    EMBO J. 2000 Jun 15;19(12):3060-8 PMID: 10856249
  3. Redundant roles for the TFIID and SAGA complexes in global transcription.
    Nature. 2000 Jun 8;405(6787):701-4 PMID: 10864329
  4. Cyclophilin A and Ess1 interact with and regulate silencing by the Sin3-Rpd3 histone deacetylase.
    EMBO J. 2000 Jul 17;19(14):3739-49 PMID: 10899127
  5. Phosphorylation of linker histone H1 regulates gene expression in vivo by creating a charge patch.
    Mol Cell. 2000 Aug;6(2):225-31 PMID: 10983971
  6. Genomic expression programs in the response of yeast cells to environmental changes.
    Mol Biol Cell. 2000 Dec;11(12):4241-57 PMID: 11102521
  7. 25 years after the nucleosome model: chromatin modifications.
    Trends Biochem Sci. 2000 Dec;25(12):619-23 PMID: 11116189
  8. Genome-wide location and function of DNA binding proteins.
    Science. 2000 Dec 22;290(5500):2306-9 PMID: 11125145
  9. Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3[middle dot]Rpd3 histone deacetylase complex and is required for histone deacetylase activity.
    J Biol Chem. 2000 Dec 29;275(52):40961-6 PMID: 11024051
  10. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.
    Nature. 2001 Jan 25;409(6819):533-8 PMID: 11206552
  11. RPD3 (REC3) mutations affect mitotic recombination in Saccharomyces cerevisiae.
    Curr Genet. 1999 Mar;35(2):68-76 PMID: 10079324
  12. Specific components of the SAGA complex are required for Gcn4- and Gcr1-mediated activation of the his4-912delta promoter in Saccharomyces cerevisiae.
    Genetics. 1999 Apr;151(4):1365-78 PMID: 10101163
  13. Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter.
    Cell. 1999 Apr 30;97(3):299-311 PMID: 10319811
  14. Chromatin-modifying and -remodeling complexes.
    Curr Opin Genet Dev. 1999 Apr;9(2):148-51 PMID: 10322131
  15. GCN5-dependent histone H3 acetylation and RPD3-dependent histone H4 deacetylation have distinct, opposing effects on IME2 transcription, during meiosis and during vegetative growth, in budding yeast.
    Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6835-40 PMID: 10359799
  16. A conserved motif present in a class of helix-loop-helix proteins activates transcription by direct recruitment of the SAGA complex.
    Mol Cell. 1999 Jul;4(1):63-73 PMID: 10445028
  17. NuA4, an essential transcription adaptor/histone H4 acetyltransferase complex containing Esa1p and the ATM-related cofactor Tra1p.
    EMBO J. 1999 Sep 15;18(18):5108-19 PMID: 10487762
  18. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity.
    Genes Dev. 1999 Sep 15;13(18):2339-52 PMID: 10500090
  19. ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS.
    Proc Natl Acad Sci U S A. 1964 May;51:786-94 PMID: 14172992
  20. Remodeling of yeast genome expression in response to environmental changes.
    Mol Biol Cell. 2001 Feb;12(2):323-37 PMID: 11179418
  21. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase.
    Mol Cell. 2000 Dec;6(6):1297-307 PMID: 11163204
  22. Gcn4 activator targets Gcn5 histone acetyltransferase to specific promoters independently of transcription.
    Mol Cell. 2000 Dec;6(6):1309-20 PMID: 11163205
  23. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.
    Nature. 2001 Mar 1;410(6824):120-4 PMID: 11242054
  24. Conversion of a gene-specific repressor to a regional silencer.
    Genes Dev. 2001 Apr 15;15(8):955-67 PMID: 11316790
  25. A role for Sds3p, a component of the Rpd3p/Sin3p deacetylase complex, in maintaining cellular integrity in Saccharomyces cerevisiae.
    Mol Genet Genomics. 2001 May;265(3):560-8 PMID: 11405640
  26. Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit.
    Science. 2001 Jun 22;292(5525):2333-7 PMID: 11423663
  27. Histone H2A.Z acetylation modulates an essential charge patch.
    Mol Cell. 2001 Jun;7(6):1329-35 PMID: 11430834
  28. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association.
    Nat Genet. 2001 Aug;28(4):327-34 PMID: 11455386
  29. SAGA is an essential in vivo target of the yeast acidic activator Gal4p.
    Genes Dev. 2001 Aug 1;15(15):1935-45 PMID: 11485988
  30. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4.
    Genes Dev. 2001 Aug 1;15(15):1946-56 PMID: 11485989
  31. Translating the histone code.
    Science. 2001 Aug 10;293(5532):1074-80 PMID: 11498575
  32. Above and within the genome: epigenetics past and present.
    J Mammary Gland Biol Neoplasia. 2001 Apr;6(2):153-67 PMID: 11501576
  33. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression.
    Mol Cell Biol. 2001 Oct;21(19):6450-60 PMID: 11533234
  34. Role of an ING1 growth regulator in transcriptional activation and targeted histone acetylation by the NuA4 complex.
    Mol Cell Biol. 2001 Nov;21(22):7629-40 PMID: 11604499
  35. Transcriptional coactivator complexes.
    Annu Rev Biochem. 2001;70:475-501 PMID: 11395415
  36. Histone modifications in transcriptional regulation.
    Curr Opin Genet Dev. 2002 Apr;12(2):142-8 PMID: 11893486
  37. Histone methylation in transcriptional control.
    Curr Opin Genet Dev. 2002 Apr;12(2):198-209 PMID: 11893494
  38. Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex.
    Genes Dev. 2002 Apr 1;16(7):806-19 PMID: 11937489
  39. Histone deacetylases as therapeutic targets in hematologic malignancies.
    Curr Opin Hematol. 2002 Jul;9(4):322-32 PMID: 12042707
  40. Methylation of histone H3 Lys 4 in coding regions of active genes.
    Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8695-700 PMID: 12060701
  41. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases.
    Cell. 2002 May 17;109(4):437-46 PMID: 12086601
  42. Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress.
    Mol Cell. 2002 Jun;9(6):1307-17 PMID: 12086627
  43. Genome-wide binding map of the histone deacetylase Rpd3 in yeast.
    Nat Genet. 2002 Jul;31(3):248-54 PMID: 12089521
  44. Exchange of N-CoR corepressor and Tip60 coactivator complexes links gene expression by NF-kappaB and beta-amyloid precursor protein.
    Cell. 2002 Jul 12;110(1):55-67 PMID: 12150997
  45. Ordered recruitment: gene-specific mechanism of transcription activation.
    Mol Cell. 2002 Aug;10(2):227-36 PMID: 12191469
  46. RPD3 is required for the inactivation of yeast ribosomal DNA genes in stationary phase.
    EMBO J. 2002 Sep 16;21(18):4959-68 PMID: 12234935
  47. Active genes are tri-methylated at K4 of histone H3.
    Nature. 2002 Sep 26;419(6905):407-11 PMID: 12353038
  48. Transcriptional regulatory networks in Saccharomyces cerevisiae.
    Science. 2002 Oct 25;298(5594):799-804 PMID: 12399584
  49. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes.
    Cell. 2002 Nov 1;111(3):369-79 PMID: 12419247
  50. Requirement of Hos2 histone deacetylase for gene activity in yeast.
    Science. 2002 Nov 15;298(5597):1412-4 PMID: 12434058
  51. Controlling the double helix.
    Nature. 2003 Jan 23;421(6921):448-53 PMID: 12540921
  52. Rfm1, a novel tethering factor required to recruit the Hst1 histone deacetylase for repression of middle sporulation genes.
    Mol Cell Biol. 2003 Mar;23(6):2009-16 PMID: 12612074
  53. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity.
    Mol Cell. 2003 Mar;11(3):709-19 PMID: 12667453
  54. The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation.
    Mol Cell. 2003 Mar;11(3):721-9 PMID: 12667454
  55. Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation.
    Cell. 2003 May 16;113(4):429-32 PMID: 12757703
  56. MYC recruits the TIP60 histone acetyltransferase complex to chromatin.
    EMBO Rep. 2003 Jun;4(6):575-80 PMID: 12776177
  57. Yeast enhancer of polycomb defines global Esa1-dependent acetylation of chromatin.
    Genes Dev. 2003 Jun 1;17(11):1415-28 PMID: 12782659
  58. NAD+-dependent deacetylase Hst1p controls biosynthesis and cellular NAD+ levels in Saccharomyces cerevisiae.
    Mol Cell Biol. 2003 Oct;23(19):7044-54 PMID: 12972620
  59. Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae.
    Mol Cell Biol. 2004 Jan;24(2):757-64 PMID: 14701747
  60. In vivo target of a transcriptional activator revealed by fluorescence resonance energy transfer.
    Genes Dev. 2004 Feb 1;18(3):333-43 PMID: 14871930
  61. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae.
    Mol Cell. 2004 Feb 27;13(4):573-85 PMID: 14992726
  62. E2F-dependent histone acetylation and recruitment of the Tip60 acetyltransferase complex to chromatin in late G1.
    Mol Cell Biol. 2004 May;24(10):4546-56 PMID: 15121871
  63. Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation.
    EMBO J. 2004 Jul 7;23(13):2597-607 PMID: 15175650
  64. Yeast histone H4 N-terminal sequence is required for promoter activation in vivo.
    Cell. 1991 Jun 14;65(6):1023-31 PMID: 2044150
  65. Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription.
    Cell. 1992 Feb 7;68(3):573-83 PMID: 1339306
  66. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation.
    Cell. 1996 Mar 22;84(6):843-51 PMID: 8601308
  67. Reversible oligonucleosome self-association: dependence on divalent cations and core histone tail domains.
    Biochemistry. 1996 Apr 2;35(13):4009-15 PMID: 8672434
  68. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast.
    Nature. 1996 Dec 12;384(6609):589-91 PMID: 8955276
  69. The TAF(II)250 subunit of TFIID has histone acetyltransferase activity.
    Cell. 1996 Dec 27;87(7):1261-70 PMID: 8980232
  70. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters.
    Cell. 1997 May 2;89(3):365-71 PMID: 9150136
  71. ADA1, a novel component of the ADA/GCN5 complex, has broader effects than GCN5, ADA2, or ADA3.
    Mol Cell Biol. 1997 Jun;17(6):3220-8 PMID: 9154821
  72. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex.
    Genes Dev. 1997 Jul 1;11(13):1640-50 PMID: 9224714
  73. A large protein complex containing the yeast Sin3p and Rpd3p transcriptional regulators.
    Mol Cell Biol. 1997 Aug;17(8):4852-8 PMID: 9234741
  74. Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo.
    Genes Dev. 1998 Mar 15;12(6):797-805 PMID: 9512514
  75. ESA1 is a histone acetyltransferase that is essential for growth in yeast.
    Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3561-5 PMID: 9520405
  76. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3.
    Nature. 1998 Apr 23;392(6678):831-5 PMID: 9572144
  77. SAP30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex.
    Mol Cell. 1998 Jun;1(7):1021-31 PMID: 9651585
  78. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III.
    Mol Cell Biol. 1998 Aug;18(8):4629-38 PMID: 9671473
  79. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo.
    Mol Cell Biol. 1998 Sep;18(9):5121-7 PMID: 9710596
  80. Enhanced transcription factor access to arrays of histone H3/H4 tetramer.DNA complexes in vitro: implications for replication and transcription.
    Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12169-73 PMID: 9770458
  81. Dissecting the regulatory circuitry of a eukaryotic genome.
    Cell. 1998 Nov 25;95(5):717-28 PMID: 9845373
  82. yTAFII61 has a general role in RNA polymerase II transcription and is required by Gcn4p to recruit the SAGA coactivator complex.
    Mol Cell. 1998 Nov;2(5):683-92 PMID: 9844640
  83. Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TATA-binding protein interaction.
    Mol Cell Biol. 1999 Jan;19(1):86-98 PMID: 9858534
  84. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae.
    EMBO J. 1999 Nov 15;18(22):6448-54 PMID: 10562556
  85. The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo.
    Genes Dev. 1999 Nov 15;13(22):2940-5 PMID: 10580001
  86. The language of covalent histone modifications.
    Nature. 2000 Jan 6;403(6765):41-5 PMID: 10638745
Article Info
Journal
Molecular cell
Abbr.
Mol Cell
ISSN
1097-2765
DOI
10.1016/j.molcel.2004.09.021
Email
francois.robert@ircm.qc.ca
Published
2004-10-22
Pages
199-209
Language
English
Region
United States
NLM ID
9802571
PMCID
PMC3004369
Subset
IM
Grants
NHGRI NIH HHS · R01 HG002668 · United States
NHGRI NIH HHS · R01 HG002668-01 · United States
External Links
PubMed source DOI: 10.1016/j.molcel.2004.09.021 PMC Full Text View journal details
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