CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation

CDK9 is a kinase critical for the productive transcription of protein-coding genes by RNA polymerase II (pol II). As part of P-TEFb, CDK9 phosphorylates the carboxyl-terminal domain (CTD) of pol II and elongation factors, which allows pol II to elongate past the early elongation checkpoint (EEC) encountered soon after initiation. We show that, in addition to halting pol II at the EEC, loss of CDK9 activity causes premature termination of transcription across the last exon, loss of polyadenylation factors from chromatin, and loss of polyadenylation of nascent transcripts. Inhibition of the phosphatase PP2A abrogates the premature termination and loss of polyadenylation caused by CDK9 inhibition, indicating that this kinase/phosphatase pair regulates transcription elongation and RNA processing at the end of protein-coding genes. We also confirm the splicing factor SF3B1 as a target of CDK9 and show that SF3B1 in complex with polyadenylation factors is lost from chromatin after CDK9 inhibition. These results emphasize the important roles that CDK9 plays in coupling transcription elongation and termination to RNA maturation downstream of the EEC. mNET-seq of total RNA polymerase II in HeLa cells treated with DMSO or the CDK9 inhibitor, DRB, for 5, 10, 15, or 30 minutes. Nuclear 3'seq in HeLa cells treated for 30 minutes with DMSO or DRB, or for 30 minutes with TNFα followed by 30 minutes with DMSO or DRB. Mouse spiked-in total RNA polymerase II ChIP-seq in HeLa cells treated with DMSO; the CDK9 inhibitor, DRB; the PP2A inhibitor, Calyculin A (CA); or DRB & CA for 30 minutes.