Dual Modes of Gene Regulation by CDK12

The process of transcription is driven forward by the activity of kinases including CDK7, CDK9 and CDK12. Accordingly, acute inhibition of any of these kinases results in profound downregulation of gene expression. Here,we discover that loss or inhibition of CDK12 also significantly upregulates a set of coding and non-coding loci, whose activation could contribute to the anti-proliferative effects of CDK12 inhibitors. Mechanistically, CDK12 inhibition impairs transcription elongation, leading to increased RNA polymerase II termination or arrest in long genes. However, short genes such as MYC and enhancer RNAs are highly transcribed in the absence of CDK12 activity. Indeed, in HER2+ breast cancer, a malignancy where CDK12 is invariably co-amplified with HER2 and its expression correlates with disease status, CDK12 inhibition markedly elevates MYC expression to induce lethality. The dual effects of CDK12 inhibition elucidated herein clarify its role in transcriptional control and have significant translational implications. Overall design: To investigate the impact of CDK12 inhibition on RNAPII behavior, PRO-seq was performed over HCC1954 cells +/- THZ531 (N=2, 200 nM, 2h). Cells were permeabilized as in Mimoso et al. 2024; run-ons were performed with biotinylated NTPs and then purified. Purified biotinylated RNAs were ligated to sequencing adapters and amplified by PCR.