CDK7 inhibition suppresses RNA polymerase II re-initiation and triggers degradation of elongation and 3'-end processing factors

CDK7 regulates RNA polymerase II (RNAPII) initiation, elongation, and termination through incompletely-defined mechanisms. Biochemical reconstitution of RNAPII transcription initiation showed that CDK7 inhibition suppressed RNAPII activity by blocking promoter escape and re-initiation and this was Mediator- and TFIID-dependent. These in vitro results were consistent with genomics and transcriptomics experiments in human cells; CDK7 inhibition globally reduced transcription and increased RNAPII promoter-proximal pausing. Moreover, we observed termination defects in CDK7-inhibited cells; unexpectedly, this coincided with rapid, widespread degradation of elongation and 3'-end processing factors. Collectively, these mechanistic insights further define how CDK7 kinase activity regulates RNAPII initiation, termination, and RNA processing. Chromatin immunoprecipitation (ChIP-seq) of human RNA Polymerase II and RNA Polymerase II phosphomarks (p-Ser5, p-Ser2, and p-Ser7) under control and CDK7-inhibited conditions.