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Series GSE100040 Query DataSets for GSE100040
Status Public on Aug 01, 2017
Title Human TFIIH kinase CDK7 regulates transcription-associated epigenetic modification
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary CDK7 phosphorylates the RNA polymerase II (pol II) CTD and activates the P-TEFb- associated kinase, CDK9, but its regulatory roles remain obscure. Using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3'-ends upon CDK7 inhibition. We also found that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5'-ends and H3K36me3 was displaced toward gene 3'-ends in CDK7as cells. Together, these results implicate a CDK7-dependent "CTD code" that regulates epigenetic marks in addition to RNA processing and pol II pausing.
Overall design WT and analogue sensitive Cdk7as mutant cells were treated with the ATP analogue NM-PP1 that specifically inhibits the Cdk7as mutant kinase. Using ChIP-seq and RNA-seq we tested the effects of Cdk7 inactivation on pol II distribution along genes, CTD Ser2 and Ser5 phosphorylation, capping enzyme recruitment, histone H3K4 and H3K36 methylation and mRNA expression
Contributor(s) Bentley D, Erickson B
Citation(s) 28768201
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM063873 Elongation and termination of transcripts by RNA pol II UNIVERSITY OF COLORADO DENVER DAVID Leonard BENTLEY
R35 GM118051 Coupling of transcription with nascent pre-mRNA metabolism UNIVERSITY OF COLORADO DENVER DAVID Leonard BENTLEY
Submission date Jun 14, 2017
Last update date Jul 25, 2021
Contact name David L. Bentley
Organization name U. Colorado School of Medicine
Department Biochemistry and Mol. Genetics
Street address 12801 E. 17th Ave
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (34)
GSM2670975 RNA pol II ChIP-seq WT Rep1
GSM2670976 RNA pol II ChIP-seqCdk7as Rep1
GSM2670977 RNA pol II ChIP-seq WT Rep2
BioProject PRJNA390543
SRA SRP109292

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GSE100040_RAW.tar 4.4 Gb (http)(custom) TAR (of BW, TDF)
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Raw data are available in SRA
Processed data provided as supplementary file

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