Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases.
Yeast contains a family of five related histone deacetylases (HDACs) whose functions are known at few genes. Therefore, we used chromatin immunoprecipitation and intergenic microarrays to generate genome-wide HDAC enzyme activity maps. Rpd3 and Hda1 deacetylate mainly distinct promoters and gene classes where they are recruited largely by novel mechanisms. Hda1 also deacetylates subtelomeric domains containing normally repressed genes that are used instead for gluconeogenesis, growth on carbon sources other than glucose, and adverse growth conditions. These domains have certain features of heterochromatin but are distinct from subtelomeric heterochromatin repressed by the deacetylase Sir2. Finally, Hos1/Hos3 and Hos2 preferentially affect ribosomal DNA and ribosomal protein genes, respectively. Thus, acetylation microarrays uncover the "division of labor" for yeast histone deacetylases.
Robyr
Daniel
D
Department of Biological Chemistry, UCLA School of Medicine and the Molecular Biology Institute, Boyer Hall, 90095, USA.
Suka
Yuko
Y
Xenarios
Ioannis
I
Kurdistani
Siavash K
SK
Wang
Amy
A
Suka
Noriyuki
N
Grunstein
Michael
M
D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D004247:DNA / Q000235:genetics / Q000378:metabolism; D004275:DNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015971:Gene Expression Regulation, Enzymologic / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D016681:Genome, Fungal; D006570:Heterochromatin / Q000235:genetics / Q000378:metabolism; D006655:Histone Deacetylases / Q000235:genetics* / Q000378:metabolism*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D047908:Intracellular Signaling Peptides and Proteins; D009687:Nuclear Proteins; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins; D017434:Protein Structure, Tertiary / Q000235:genetics; D012097:Repressor Proteins; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D029702:Schizosaccharomyces pombe Proteins; D014157:Transcription Factors
D002352:Carrier Proteins; D004275:DNA, Ribosomal; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D006570:Heterochromatin; D006657:Histones; C421189:Hos2 protein, S pombe; D047908:Intracellular Signaling Peptides and Proteins; D009687:Nuclear Proteins; D010940:Plant Proteins; D012097:Repressor Proteins; D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins; D029702:Schizosaccharomyces pombe Proteins; D014157:Transcription Factors; D004247:DNA; C499673:HDA1 protein, S cerevisiae; C071665:RPD3 protein, S cerevisiae; D006655:Histone Deacetylases