title: Genome-wide association of mediator and RNA polymerase II in wild-type and mediator mutant yeast.
abstract: Mediator is a large, multisubunit complex that is required for essentially all mRNA transcription in eukaryotes. In spite of the importance of Mediator, the range of its targets and how it is recruited to these is not well understood. Previous work showed that in Saccharomyces cerevisiae, Mediator contributes to transcriptional activation by two distinct mechanisms, one depending on the tail module triad and favoring SAGA-regulated genes, and the second occurring independently of the tail module and favoring TFIID-regulated genes. Here, we use chromatin immunoprecipitation sequencing (ChIP-seq) to show that dependence on tail module subunits for Mediator recruitment and polymerase II (Pol II) association occurs preferentially at SAGA-regulated over TFIID-regulated genes on a genome-wide scale. We also show that recruitment of tail module subunits to active gene promoters continues genome-wide when Mediator integrity is compromised in med17 temperature-sensitive (ts) yeast, demonstrating the modular nature of the Mediator complex in vivo. In addition, our data indicate that promoters exhibiting strong and stable occupancy by Mediator have a wide range of activity and are enriched for targets of the Tup1-Cyc8 repressor complex. We also identify a number of strong Mediator occupancy peaks that overlap dubious open reading frames (ORFs) and are likely to include previously unrecognized upstream activator sequences.
authors.affiliation: Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Paul
authors.affiliation: Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA.
authors.forename: Z Iris
authors.initials: ZI
authors.lastname: Zhu
authors.affiliation: Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA landsman@ncbi.nlm.nih.gov randall.morse@health.ny.gov.
authors.forename: David
authors.initials: D
authors.lastname: Landsman
authors.affiliation: Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA Department of Biomedical Science, University at Albany School of Public Health, Albany, New York, USA landsman@ncbi.nlm.nih.gov randall.morse@health.ny.gov.
authors.forename: Randall H
authors.initials: RH
authors.lastname: Morse
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D015966:Gene Expression Regulation, Fungal; D056892:Mediator Complex / Q000235:genetics / Q000378:metabolism*; D009154:Mutation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D056892:Mediator Complex; D029701:Saccharomyces cerevisiae Proteins; D012319:RNA Polymerase II