title: Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription.
abstract: Yeast Rpd3 histone deacetylase plays an important role at actively transcribed genes. We characterized two distinct Rpd3 complexes, Rpd3L and Rpd3S, by MudPIT analysis. Both complexes shared a three subunit core and Rpd3L contains unique subunits consistent with being a promoter targeted corepressor. Rco1 and Eaf3 were subunits specific to Rpd3S. Mutants of RCO1 and EAF3 exhibited increased acetylation in the FLO8 and STE11 open reading frames (ORFs) and the appearance of aberrant transcripts initiating within the body of these ORFs. Mutants in the RNA polymerase II-associated SET2 histone methyltransferase also displayed these defects. Set2 functioned upstream of Rpd3S and the Eaf3 methyl-histone binding chromodomain was important for recruitment of Rpd3S and for deacetylation within the STE11 ORF. These data indicate that Pol II-associated Set2 methylates H3 providing a transcriptional memory which signals for deacetylation of ORFs by Rpd3S. This erases transcription elongation-associated acetylation to suppress intragenic transcription initiation.
authors.affiliation: Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Carrozza
authors.forename: Bing
authors.initials: B
authors.lastname: Li
authors.forename: Laurence
authors.initials: L
authors.lastname: Florens
authors.forename: Tamaki
authors.initials: T
authors.lastname: Suganuma
authors.forename: Selene K
authors.initials: SK
authors.lastname: Swanson
authors.forename: Kenneth K
authors.initials: KK
authors.lastname: Lee
authors.forename: Wei-Jong
authors.initials: WJ
authors.lastname: Shia
authors.forename: Scott
authors.initials: S
authors.lastname: Anderson
authors.forename: John
authors.initials: J
authors.lastname: Yates
authors.forename: Michael P
authors.initials: MP
authors.lastname: Washburn
authors.forename: Jerry L
authors.initials: JL
authors.lastname: Workman
mesh_terms: D000107:Acetylation; D000123:Acetyltransferases / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D015966:Gene Expression Regulation, Fungal; D006655:Histone Deacetylases / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D020930:MAP Kinase Kinase Kinases / Q000235:genetics / Q000378:metabolism; D008745:Methylation; D008780:Methyltransferases / Q000235:genetics / Q000378:metabolism*; D008970:Molecular Weight; D009154:Mutation / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D021122:Protein Subunits / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D006657:Histones; D021122:Protein Subunits; D012097:Repressor Proteins; C071731:SIN3 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D008780:Methyltransferases; C448996:Set2 protein, S cerevisiae; D000123:Acetyltransferases; C428131:Eaf3 protein, S cerevisiae; D020930:MAP Kinase Kinase Kinases; C067018:Ste11 protein, S cerevisiae; C071665:RPD3 protein, S cerevisiae; D006655:Histone Deacetylases