Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast.
We have conducted a genomewide investigation into the enzymatic specificity, expression profiles, and binding locations of four histone deacetylases (HDACs), representing the three different phylogenetic classes in fission yeast (Schizosaccharomyces pombe). By directly comparing nucleosome density, histone acetylation patterns and HDAC binding in both intergenic and coding regions with gene expression profiles, we found that Sir2 (class III) and Hos2 (class I) have a role in preventing histone loss; Clr6 (class I) is the principal enzyme in promoter-localized repression. Hos2 has an unexpected role in promoting high expression of growth-related genes by deacetylating H4K16Ac in their open reading frames. Clr3 (class II) acts cooperatively with Sir2 throughout the genome, including the silent regions: rDNA, centromeres, mat2/3 and telomeres. The most significant acetylation sites are H3K14Ac for Clr3 and H3K9Ac for Sir2 at their genomic targets. Clr3 also affects subtelomeric regions which contain clustered stress- and meiosis-induced genes. Thus, this combined genomic approach has uncovered different roles for fission yeast HDACs at the silent regions in repression and activation of gene expression.
Wirén
Marianna
M
Karolinska Institutet, Department of Biosciences/School of Life Sciences, University College Sodertorn, Huddinge, Sweden.
Silverstein
Rebecca A
RA
Sinha
Indranil
I
Walfridsson
Julian
J
Lee
Hang-Mao
HM
Laurenson
Patricia
P
Pillus
Lorraine
L
Robyr
Daniel
D
Grunstein
Michael
M
Ekwall
Karl
K
D000107:Acetylation; D018797:Cell Cycle Proteins / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D006655:Histone Deacetylases / Q000235:genetics* / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D009707:Nucleosomes / Q000201:enzymology*; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D012568:Schizosaccharomyces; D029702:Schizosaccharomyces pombe Proteins / Q000378:metabolism; D037761:Sirtuins / Q000378:metabolism
D018797:Cell Cycle Proteins; C115303:Clr6 protein, S pombe; D006657:Histones; C421189:Hos2 protein, S pombe; D009707:Nucleosomes; D029702:Schizosaccharomyces pombe Proteins; D037761:Sirtuins; D006655:Histone Deacetylases