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Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions
Karolinska Institutet.
Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
Institute of Molecular Biology, Copenhagen, Denmark.
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2006 (Engelska)Ingår i: Molecular Cell, ISSN 1097-2765, E-ISSN 1097-4164, Vol. 22, nr 2, s. 169-178Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

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.

Ort, förlag, år, upplaga, sidor
2006. Vol. 22, nr 2, s. 169-178
Nationell ämneskategori
Biokemi och molekylärbiologi Cellbiologi
Identifikatorer
URN: urn:nbn:se:sh:diva-14301DOI: 10.1016/j.molcel.2006.03.032ISI: 000237150400007PubMedID: 16630887Scopus ID: 2-s2.0-33646075157OAI: oai:DiVA.org:sh-14301DiVA, id: diva2:468148
Tillgänglig från: 2011-12-20 Skapad: 2011-12-20 Senast uppdaterad: 2017-12-08Bibliografiskt granskad
Ingår i avhandling
1. Genome-wide study of HDACs and transcription in Schizosaccharomyces pombe
Öppna denna publikation i ny flik eller fönster >>Genome-wide study of HDACs and transcription in Schizosaccharomyces pombe
2010 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

The eukaryotic genome has to be organized to fit into the cell and this is achieved by packing of DNA into chromatin. The basic repeating structural unit of chromatin is the nucleosome, which consists of DNA wrapped around histone proteins. Histones are subjected to multiple covalent posttranslational modifications including, acetylation, methylation, phosphorylation, and ubiquitination. These modifications take part in gene regulation by changing the structure of chromatin and by recruiting gene regulatory proteins. Histone acetylation can be removed by histone deacetylases (HDACs), which are highly conserved enzymes that regulate a diverse number of biological processes including gene expression and chromosome segregation, and have shown to be closely linked to major diseases like cancer. This thesis described the genome-wide role of HDACs and transcription in S. pombe. We studied the genome wide binding targets and enzymatic specificity of different S. pombe HDACs and uncovered different roles for the enzymes at silent regions and in repression and activation of gene expression. We proposed that independent of gene length, a typical fission yeast gene shows a 5 to 3 polarity, i.e., the histone acetylation levels peak near the ATG and gradually decrease in the coding regions. We also observed that different HDACs are responsible for different position within the ORF regions. Our genome-wide study of two different Mediator complexes reviled that they displayed similar binding patterns, and interactions with promoters and upstream activating sequences correlated with increased transcription activity. We also found that Mediator associates with the downstream coding region of many genes. We finally developed a method, E-map, which made it possible to systematically construct haploid double mutants. This method was used for constructing genome-wide genetic interaction maps of HDACs in S. pombe. From our preliminary results we discovered a new link between the Class III HDACs and a biosynthesis protein. Our data also suggest that different HDACs are involved in distinct biological processes.

Ort, förlag, år, upplaga, sidor
Stockholm: Karolinska Institutet, 2010. s. 51
Nationell ämneskategori
Biologiska vetenskaper
Identifikatorer
urn:nbn:se:sh:diva-30694 (URN)978-91-7409-970-6 (ISBN)
Handledare
Tillgänglig från: 2016-08-04 Skapad: 2016-08-04 Senast uppdaterad: 2016-08-04Bibliografiskt granskad

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Wirén, MariannaSinha, IndranilEkwall, Karl

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Molecular Cell
Biokemi och molekylärbiologiCellbiologi

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