title: Genome-wide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters.
abstract: In Saccharomyces cerevisiae, TFIID and SAGA principally mediate transcription of constitutive housekeeping genes and stress-inducible genes, respectively, by delivering TBP to the core promoter. Both are multi-protein complexes composed of 15 and 20 subunits, respectively, five of which are common and which may constitute a core sub-module in each complex. Although genome-wide gene expression studies have been conducted extensively in several TFIID and/or SAGA mutants, there are only a limited number of studies investigating genome-wide localization of the components of these two complexes. Specifically, there are no previous reports on localization of a complete set of Tafs and the effects of taf mutations on localization. Here, we examine the localization profiles of a complete set of Tafs, Gcn5, Bur6/Ncb2, Sua7, Tfa2, Tfg1, Tfb3 and Rpb1, on chromosomes III, IV and V by chromatin immunoprecipitation (ChIP)-chip analysis in wild-type and taf1-T657K mutant strains. In addition, we conducted conventional and sequential ChIP analysis of several ribosomal protein genes (RPGs) and non-RPGs. Intriguingly, the results revealed a novel relationship between TFIIB and NC2, simultaneous co-localization of SAGA and TFIID on RPG promoters, specific effects of taf1 mutation on Taf2 occupancy, and an indirect evidence for the existence of different TFIID conformations.
authors.affiliation: Division of Molecular and Cellular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan.
authors.forename: Kazushige
authors.initials: K
authors.lastname: Ohtsuki
authors.forename: Koji
authors.initials: K
authors.lastname: Kasahara
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Shirahige
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Kokubo
mesh_terms: D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D009154:Mutation; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012097:Repressor Proteins / Q000032:analysis; D012269:Ribosomal Proteins / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis* / Q000235:genetics* / Q000378:metabolism; D035381:TATA-Binding Protein Associated Factors / Q000032:analysis* / Q000235:genetics* / Q000378:metabolism; D015534:Trans-Activators / Q000032:analysis; D035581:Transcription Factor TFIIB / Q000032:analysis / Q000378:metabolism; D035362:Transcription Factor TFIID / Q000032:analysis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: C403190:BUR6 protein, S cerevisiae; D012097:Repressor Proteins; D012269:Ribosomal Proteins; C507785:SAGA complex, S cerevisiae; C073680:SUA7 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; C106785:TAF1 protein, S cerevisiae; C087176:TAF2 protein, S cerevisiae; D035381:TATA-Binding Protein Associated Factors; D015534:Trans-Activators; D035581:Transcription Factor TFIIB; D035362:Transcription Factor TFIID