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Series GSE62171 Query DataSets for GSE62171
Status Public on Dec 11, 2015
Title RNA Polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA Polymerase II
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Release of promoter-proximal paused RNA polymerase II (Pol II) during early elongation is a critical step in transcriptional regulation in metazoan cells. Paused Pol II release is thought to require the kinase activity of cyclin-dependent kinase 9 (CDK9) for the phosphorylation of DRB sensitivity-inducing factor, negative elongation factor, and C-terminal domain (CTD) serine-2 of Pol II. We found that Pol II-associated factor 1 (PAF1) is a critical regulator of paused Pol II release, that positive transcription elongation factor b (P-TEFb) directly regulates the initial recruitment of PAF1 complex (PAF1C) to genes, and that the subsequent recruitment of CDK12 is dependent on PAF1C. These findings reveal cooperativity among P-TEFb, PAF1C, and CDK12 in pausing release and Pol II CTD phosphorylation.
Overall design Comparison of the chromatin occupancy of [1] PAF1, CDC73, LEO1, CTR9, total Pol II, and CTD serine 2-phosphorylated Pol II by ChIP-seq in THP1 cells; [2] PAF1, Pol II, Pol II (ser-5p), CDK12, and CDK9 by ChIP-seq in control and PAF1 knockdown cells; [3] LEO1 and Pol II by ChIP-seq in control and flavopiridol treated THP1 cells.
Contributor(s) Yu M, Yang W, Ni T, Tang Z, Nakadai T, Zhu J, Roeder RG
Citation(s) 26659056
Submission date Oct 08, 2014
Last update date May 15, 2019
Contact name Robert Roeder
Organization name The Rockefeller University
Street address 1230 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (32)
GSM1520903 Control-1-THP1 RNAseq
GSM1520904 Control-2-THP1 RNAseq
GSM1520905 PAF1KD-1-THP1 RNAseq
BioProject PRJNA263366
SRA SRP048744

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Supplementary file Size Download File type/resource
GSE62171_RAW.tar 1.1 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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