RT Journal Article
SR Electronic
T1 CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 483958
DO 10.1101/483958
A1 Malgorzata Krajewska
A1 Ruben Dries
A1 Andrew V. Grassetti
A1 Sofia Dust
A1 Yang Gao
A1 Hao Huang
A1 Bandana Sharma
A1 Daniel S. Day
A1 Nicholas Kwiatkowski
A1 Monica Pomaville
A1 Oliver Dodd
A1 Edmond Chipumuro
A1 Tinghu Zhang
A1 Arno L. Greenleaf
A1 Guo-Cheng Yuan
A1 Nathanael S. Gray
A1 Richard A. Young
A1 Matthias Geyer
A1 Scott A. Gerber
A1 Rani E. George
YR 2018
UL http://biorxiv.org/content/early/2018/11/30/483958.abstract
AB The cyclin-dependent kinase 12 (CDK12) modulates transcription elongation by phosphorylating the carboxy-terminal domain of RNA polymerase II and appears to selectively affect the expression of DNA damage response (DDR) and mRNA processing genes. Yet, the mechanism(s) by which it achieves this selectivity remains unclear. Using a highly selective CDK12/13 inhibitor, THZ531, and nascent RNA sequencing, we show that CDK12 inhibition results in gene length-dependent elongation defects, leading to premature cleavage and polyadenylation (PCPA) as well as loss of expression of long (>45 kb) genes, a substantial proportion of which participate in the DDR. This early termination phenotype correlated with an increased proportion of intronic polyadenylation sites, a feature that was especially prominent among DDR genes. Finally, phosphoproteomic analysis indicated that pre-mRNA processing factors, including those involved in PCPA, are direct phosphotargets of CDKs 12 and 13. These results support a model in which DDR genes are uniquely susceptible to CDK12 inhibition due primarily to their relatively longer lengths and lower ratios of U1 snRNP binding to intronic polyadenylation sites.