title: Ubp8p, a histone deubiquitinase whose association with SAGA is mediated by Sgf11p, differentially regulates lysine 4 methylation of histone H3 in vivo.
abstract: Despite recent advances in characterizing the regulation of histone H3 lysine 4 (H3-K4) methylation at the GAL1 gene by the H2B-K123-specific deubiquitinase activity of Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-acetyltransferase)-associated Ubp8p, our knowledge on the general role of Ubp8p at the SAGA-dependent genes is lacking. For this study, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation (ChIP) assay, we have analyzed the role of Ubp8p in the regulation of H3-K4 methylation at three other SAGA-dependent yeast genes, namely, PHO84, ADH1, and CUP1. Like that at GAL1, H3-K4 methylation is increased at the PHO84 core promoter in the UBP8 deletion mutant. We also show that H3-K4 methylation remains invariant at the PHO84 open reading frame in the Deltaubp8 mutant, demonstrating a highly localized role of Upb8p in regulation of H3-K4 methylation at the promoter in vivo. However, unlike that at PHO84, H3-K4 methylation at the two other SAGA-dependent genes is not controlled by Ubp8p. Interestingly, Ubp8p and H3-K4 methylation are dispensable for preinitiation complex assembly at the core promoters of these genes. Our ChIP assay further demonstrates that the association of Ubp8p with SAGA is mediated by Sgf11p, consistent with recent biochemical data. Collectively, the data show that Ubp8p differentially controls H3-K4 methylation at the SAGA-dependent promoters, revealing a complex regulatory network of histone methylation in vivo.
authors.affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
authors.forename: Abhijit
authors.initials: A
authors.lastname: Shukla
authors.forename: Nadia
authors.initials: N
authors.lastname: Stanojevic
authors.forename: Zhen
authors.initials: Z
authors.lastname: Duan
authors.forename: Payel
authors.initials: P
authors.lastname: Sen
authors.forename: Sukesh R
authors.initials: SR
authors.lastname: Bhaumik
mesh_terms: D000426:Alcohol Dehydrogenase / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D010450:Endopeptidases / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D008239:Lysine / Q000378:metabolism; D008668:Metallothionein; D008745:Methylation; D009154:Mutation; D011401:Promoter Regions, Genetic; D028081:Proton-Phosphate Symporters / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D015534:Trans-Activators / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D025801:Ubiquitin / Q000378:metabolism
chemical_list: C500769:CUP1-1 protein, S cerevisiae; D002352:Carrier Proteins; D006657:Histones; C105495:PHO84 protein, S cerevisiae; D028081:Proton-Phosphate Symporters; C507785:SAGA complex, S cerevisiae; C489245:SGF11 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D025801:Ubiquitin; D008668:Metallothionein; D000426:Alcohol Dehydrogenase; D010450:Endopeptidases; C503322:UBP8 protein, S cerevisiae; D008239:Lysine