CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation

• Published in: Nature communications Vol. 10; no. 1; p. 1757
• Main Authors: Krajewska, Malgorzata, Dries, Ruben, Grassetti, Andrew V., Dust, Sofia, Gao, Yang, Huang, Hao, Sharma, Bandana, Day, Daniel S., Kwiatkowski, Nicholas, Pomaville, Monica, Dodd, Oliver, Chipumuro, Edmond, Zhang, Tinghu, Greenleaf, Arno L., Yuan, Guo-Cheng, Gray, Nathanael S., Young, Richard A., Geyer, Matthias, Gerber, Scott A., George, Rani E.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 15.04.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 49/31; 49/39; 49/61; 49/90; 49/91; 631/337/572; 631/337/572/2102; 631/67/1059/602; 82/58; 82/83; 96/106; 96/2; 96/63; Cancer; Cell Line, Tumor; Chromatography, High Pressure Liquid; Chromatography, Liquid; Cleavage; Cyclin-dependent kinase; Cyclin-dependent kinases; Cyclin-Dependent Kinases - genetics; Deoxyribonucleic acid; DNA; DNA Damage; DNA Repair - genetics; DNA-directed RNA polymerase; Elongation; Gene expression; Genes; Humanities and Social Sciences; Humans; Inhibition; Kinases; Models, Molecular; mRNA processing; multidisciplinary; Mutation; Phenotypes; Phosphorylation; Polyadenylation; Post-transcription; Ribonucleic acid; Ribonucleoproteins (small nuclear); RNA; RNA polymerase; RNA polymerase II; RNA Processing, Post-Transcriptional; Science; Science (multidisciplinary); Selectivity; Tandem Mass Spectrometry; Transcription elongation
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-09703-y

Cyclin-dependent kinase 12 (CDK12) modulates transcription elongation by phosphorylating the carboxy-terminal domain of RNA polymerase II and selectively affects the expression of genes involved in the DNA damage response (DDR) and mRNA processing. Yet, the mechanisms underlying such selectivity remain unclear. Here we show that CDK12 inhibition in cancer cells lacking CDK12 mutations results in gene length-dependent elongation defects, inducing premature cleavage and polyadenylation (PCPA) and loss of expression of long (>45 kb) genes, a substantial proportion of which participate in the DDR. This early termination phenotype correlates with an increased number of intronic polyadenylation sites, a feature especially prominent among DDR genes. Phosphoproteomic analysis indicated that CDK12 directly phosphorylates pre-mRNA processing factors, including those regulating PCPA. These results support a model in which DDR genes are uniquely susceptible to CDK12 inhibition primarily due to their relatively longer lengths and lower ratios of U1 snRNP binding to intronic polyadenylation sites. Cdk12 is primarily involved in the regulation of DNA damage response (DDR) gene transcription as well as mRNA processing. Here, the authors demonstrate that CDK12 suppresses intronic polyadenylation, and that inhibition of this kinase primarily affects the expression of long genes with higher numbers of polyA sites, features common to many DDR genes.