Abstract
The transition of RNA polymerase II (Pol II) from transcription initiation into productive elongation in eukaryotic cells is regulated by the P-TEFb kinase, which phosphorylates the C-terminal domain of paused Pol II at promoter-proximal regions. Our recent study found that P-TEFb (in an inhibited state bound to the 7SK snRNP complex) interacts with the KAP1/TRIM28 transcriptional regulator, and that KAP1 and the 7SK snRNP co-occupy most gene promoters containing paused Pol II. Here we provide a detailed experimental description and analysis of the ChIP-seq datasets that have been deposited into Gene Expression Omnibus (GEO): GS72622, so that independent groups can replicate and expand upon these findings. We propose these datasets would provide valuable information for researchers studying mechanisms of transcriptional regulation including Pol II pausing and pause release.
Highlights
The transition of RNA polymerase II (Pol II) from transcription initiation into productive elongation in eukaryotic cells is regulated by the positive transcription elongation factor b (P-TEFb) kinase, which phosphorylates the C-terminal domain of paused Pol II at promoter-proximal regions
We found that paused Pol II is present at the promoter-proximal region of 17,316 genes, and that the Kruppel-associated protein (KAP1)-7SK small nuclear ribonucleoprotein (snRNP) is present at the promoter proximal-region of 14,203 genes, which represents an intersection of 12,211 genes
We described here an experimental approach to determine the occupancy of KAP1, the 7SK snRNP and Pol II in the human genome
Summary
The human colorectal HCT116 cell line (obtained from ATCC) was maintained (at a confluency not greater than 90%) in DMEM supplemented with 10% heat-inactivated FBS and 1 × penicillin/ streptomycin at 37 °C with 5% CO2.
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