CDK12 regulates co-transcriptional splicing and RNA turnover in human cells

The cyclin-dependent kinase CDK12 promotes transcription completion of long genes by suppressing the utilization of intronic polyadenylation sites that cause premature transcriptional termination. One class of genes that are particularly affected by loss of CDK12 activity are DNA damage response genes and therefore inhibitors of CDK12 have garnered interest as cancer therapeutic amplifiers. In this study, we used the CDK12/13 inhibitor THZ531 to treat HF1 (normal human fibroblasts), K562 and HeLa cells and the adenine analog 1-NM-PP1 to treat analog-sensitive HeLa cells and to assess the acute effects on transcription and RNA processing using Bru-seq and BruChase-seq. While acute transcriptional changes were small and limited to the 3'-ends of genes, RNA turnover was dramatically affected by CDK12 inhibition. Importantly, the downregulation of DNA damage response genes was predominantly due to increased mRNA turnover. Co-transcriptional splicing was suppressed by CDK12 inhibition. Finally, many introns that showed premature transcriptional termination were found to be resistant to degradation following CDK12 inhibition despite showing efficient splicing. We speculate that premature termination and addition of poly(A)s protect these spliced intronic fragments from degradation. These studies reveal previously unknown roles of CDK12 in regulating RNA turnover and co-transcriptional splicing. Overall design: The nascent RNA sequencing methods Bru-seq and BruChase-seq were used to determine co-transcriptional splicing and turnover in human cells. HeLa cells expressing anolog-sensitive CDK12 (HeLa-AS) were treated with DMSO (control) or 1NMPP1 and subject to Bru-seq (2 replicates each) or BruChase-seq (3 replicates each, 2h chase). HF1, K562, and HeLa cells were treated with either DMSO (control) or THZ531 and subject to Bru-seq (1 replicate each) or BruChase-seq (1 replicate each; 6h chase for K562 and HF1 and 2h chase for HeLa).