GSE115290
CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation
Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD. Overall design: After CDK12 inhibition for 15 minutes with 1-NM-PP1 in HEK293 CDK12as cells, we performed mNET-seq (total pol II, Ser2P (with two different antibodies), and Ser5P) and ChIP-seq for total pol II, Ser2P, Ser5P, LEO1, SPT6, and CPSF73. In wild-type HEK293 cells, we performed ChIP-seq for total pol II after treatment with DMSO or 1-NM-PP1 for 15 minutes.