title: Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions.
abstract: Mediator exists in a free form containing the Med12, Med13, CDK8, and CycC subunits (the Srb8-11 module) and a smaller form, which lacks these four subunits and associates with RNA polymerase II (Pol II), forming a holoenzyme. We use chromatin immunoprecipitation (ChIP) and DNA microarrays to investigate genome-wide localization of Mediator and the Srb8-11 module in fission yeast. Mediator and the Srb8-11 module display similar binding patterns, and interactions with promoters and upstream activating sequences correlate with increased transcription activity. Unexpectedly, Mediator also interacts with the downstream coding region of many genes. These interactions display a negative bias for positions closer to the 5' ends of open reading frames (ORFs) and appear functionally important, because downregulation of transcription in a temperature-sensitive med17 mutant strain correlates with increased Mediator occupancy in the coding region. We propose that Mediator coordinates transcription initiation with transcriptional events in the coding region of eukaryotic genes.
authors.affiliation: Department Laboratory Medicine, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Marianna
authors.initials: M
authors.lastname: Wirén
authors.forename: Indranil
authors.initials: I
authors.lastname: Sinha
authors.forename: Nina N
authors.initials: NN
authors.lastname: Rasmussen
authors.forename: Tomas
authors.initials: T
authors.lastname: Linder
authors.forename: Steen
authors.initials: S
authors.lastname: Holmberg
authors.forename: Karl
authors.initials: K
authors.lastname: Ekwall
authors.forename: Claes M
authors.initials: CM
authors.lastname: Gustafsson
mesh_terms: D000483:Alleles; D047369:Chromatin Immunoprecipitation; D004271:DNA, Fungal; D021901:DNA, Intergenic; D015536:Down-Regulation; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D016681:Genome, Fungal; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism*; D012568:Schizosaccharomyces / Q000235:genetics / Q000378:metabolism; D029702:Schizosaccharomyces pombe Proteins / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D004271:DNA, Fungal; D021901:DNA, Intergenic; D029701:Saccharomyces cerevisiae Proteins; D029702:Schizosaccharomyces pombe Proteins