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Series GSE31070 Query DataSets for GSE31070
Status Public on Dec 01, 2012
Title A positive feedback loop links opposing functions of P-TEFb/Cdk9 and histone H2B mono-ubiquitylation to regulate transcript elongation in fission yeast
Organism Schizosaccharomyces pombe
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved patterns of histone modification within transcribed regions, but it remains uncertain how these modifications influence, or are influenced by, properties of the elongation complex. Here we establish an intimate link between Cdk9, the kinase component of positive transcription elongation factor b (P-TEFb), and mono-ubiquitylation of histone H2B (H2Bub1), in the fission yeast Schizosaccharomyces pombe. Mutations that impair Cdk9 function reduce H2Bub1 levels in vivo. Conversely, mutations that prevent H2Bub1 decrease phosphorylation of elongation factor subunit Spt5, a sensitive and specific indicator of Cdk9 activity. Chromatin immunoprecipitation (ChIP) analysis suggests this is due to impaired Cdk9 recruitment to H2Bub1-deficient chromatin. P-TEFb and H2Bub1 pathways also interact genetically: mutation of the histone H2B ubiquitin-acceptor residue decreases the requirement for Cdk9 activity in vivo, and multiple cdk9 mutations suppress morphological defects of H2Bub1-deficient strains. Moreover, H2Bub1 loss causes redistribution of transcribing RNAPII on chromatin that is corrected by a hypomorphic cdk9 mutation. Therefore, whereas mutual dependence of Spt5 phosphorylation and H2Bub1 suggests positive feedback between P-TEFb and the ubiquitylation machinery, mutual suppression by cdk9 and H2Bub1-pathway mutations indicates an antagonistic relationship, whereby the activities must be balanced to properly regulate elongation.
 
Overall design In order to study the genome-wide localization of H2Bub1 in Schizosaccharomyces pombe, H2Bub1, H2B-Flag as well as RNAPII (along with associated DNA sequences) were immunoprecipitated using repectively anti-H2Bub1, anti-Flag and anti-8WG16 antibodies. The ChIPs were performed in duplicate from WT cells as well as in the H2B-K119R mutant. The extracted DNA was hybridized to a DNA microarray containing an average of 4 probes per kilobase across the whole yeast genome. The combined datasets are available in the supplemental files of the related publication.
 
Contributor(s) Viladevall L, Lee KM, Jacques P, Page V, Schneider S, Zhang C, Schwer B, Robert F, Fisher RP, Tanny JC
Citation(s) 22876190
Submission date Jul 31, 2011
Last update date Mar 26, 2021
Contact name François Robert
E-mail(s) Francois.Robert@ircm.qc.ca
URL http://www.ircm.qc.ca/microsites/francoisrobert/en/index.html
Organization name Institut de recherches cliniques de Montréal (IRCM)
Department Chromatin and Genomic Expression
Street address 110, avenue des Pins Ouest
City Montréal
State/province Québec
ZIP/Postal code H2W 1R7
Country Canada
 
Platforms (1)
GPL16218 Agilent-015424 S. pombe Whole Genome ChIP-on-Chip Microarray 4x44K (Feature Number version - A_86_Pnnnn probes)
Samples (6)
GSM769513 H2Bub_vs_H2B--WT_#1
GSM769514 H2Bub_vs_H2B--WT_#2
GSM769515 8WG16_vs_WCE--WT_#1
Relations
BioProject PRJNA144845

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE31070_RAW.tar 258.7 Mb (http)(custom) TAR (of GPR, TIFF)
Processed data included within Sample table

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