Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions

TY - JOUR

T1 - Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions

AU - Zhu, Xuefeng

AU - Wirén, Marianna

AU - Sinha, Indranil

AU - Rasmussen, Nina N.

AU - Linder, Tomas

AU - Holmberg, Steen

AU - Ekwall, Karl

AU - Gustafsson, Claes M

N1 - Keywords: Alleles; Chromatin Immunoprecipitation; DNA, Fungal; DNA, Intergenic; Down-Regulation; Gene Expression Profiling; Genes, Fungal; Genome, Fungal; Nucleic Acid Amplification Techniques; Oligonucleotide Array Sequence Analysis; Open Reading Frames; Promoter Regions, Genetic; Protein Binding; Reverse Transcriptase Polymerase Chain Reaction; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Schizosaccharomyces; Schizosaccharomyces pombe Proteins; Transcription, Genetic

PY - 2006

Y1 - 2006

N2 - 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.

AB - 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.

U2 - 10.1016/j.molcel.2006.03.032

DO - 10.1016/j.molcel.2006.03.032

M3 - Journal article

C2 - 16630887

SN - 1097-2765

VL - 22

SP - 169

EP - 178

JO - Molecular Cell

JF - Molecular Cell

IS - 2

ER -