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Series GSE22636 Query DataSets for GSE22636
Status Public on Nov 28, 2010
Title DSIF and RNA polymerase II CTD Phosphorylation Coordinate the Recruitment of Rpd3S to Actively Transcribed Genes
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Histone deacetylase Rpd3 is part of two distinct complexes: the large (Rpd3L) and small (Rpd3S) complexes. While Rpd3L targets specific promoters for gene repression, Rpd3S is recruited to ORFs to deacetylate histones in the wake of RNA polymerase II, to prevent cryptic initiation within genes. Methylation of histone H3 at lysine 36 by the Set2 methyltransferase is thought to mediate the recruitment of Rpd3S. Here, we confirm by ChIP-Chip that Rpd3S binds active ORFs. Surprisingly, however, Rpd3S is not recruited to all active genes, and its recruitment is Set2-independent. However, Rpd3S complexes recruited in the absence of H3K36 methylation appear to be inactive. Finally, we present evidence implicating the yeast DSIF complex (Spt4/5) and RNA polymerase II phosphorylation by Kin28 and Ctk1 in the recruitment of Rpd3S to active genes. Taken together, our data support a model where Set2-dependent histone H3 methylation is required for the activation of Rpd3S following its recruitment to the RNA polymerase II C-terminal domain.
Overall design In order to examine the genome-wide localization of RNAPII and Spt6 in Saccharomyces cerevisiae, RNAPII and Spt6 along with associated DNA sequences were immunoprecipitated using anti-8WG16 and anti-HA antibodies, respectively. The RNAPII and Spt6 chromatin immunoprecipitation was performed in duplicate from WT cells as described below. 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) Drouin S, Laramée L, Jacques P, Forest A, Bergeron M, Robert F
Citation(s) 21060864
Submission date Jun 30, 2010
Last update date Feb 15, 2018
Contact name François Robert
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 (2)
GPL3737 Agilent-012713 Yeast Whole Genome ChIP-on-chip Microarray (G4486A)
GPL4131 Agilent-014810 Yeast Whole Genome ChIP-on-Chip Microarray 4x44K (G4493A)
Samples (87)
GSM561196 RCO1-9Myc_WT_vs_NoTag_#1
GSM561197 RCO1-9Myc_WT_vs_NoTag_#2
GSM561198 RCO1-9Myc_WT_vs_NoTag_#3
BioProject PRJNA128103

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
GSE22636_RAW.tar 3.8 Gb (http)(custom) TAR (of GPR, TIFF)
Processed data included within Sample table

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