Cdk12 regulates DNA repair Genes by suppressing intronic polyadenylation
Author(s)Dubbury, Sara Jane
Massachusetts Institute of Technology. Department of Biology.
Phillip A. Sharp.
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During transcription, cyclin-dependent kinases (CDKs) dynamically phosphorylate the C-terminal domain (CTD) of RNA Polymerase II (RNAPII) to recruit factors that coordinate transcription and mRNA biogenesis. Cdk12 phosphorylates Serine 2 (Ser2) of the RNAPII CTD, a modification associated with the regulation of transcription elongation, splicing, and cleavage/polyadenylation. Unlike other transcriptional CDKs that regulate most expressed genes, Cdk12 depletion abrogates the expression of homologous recombination (HR) genes relatively specifically, suppressing the HR DNA damage repair pathway and sensitizing cells to genotoxic stresses that cause replication fork collapse, such as Parp1 inhibitors. The proposed role for Cdk12 in regulating HR is clinically significant for two reasons. First, Cdk12 loss-of-function mutations populate high-grade serous ovarian carcinoma and castration-resistant prostate tumors raising the possibility that Cdk12 mutational status may predict the effectiveness of chemotherapeutics that target HR-deficient tumors. Second, readily available small molecule inhibitors of Cdk12 induce sensitization of HR-competent tumors to Parp1 inhibitors in vivo raising the possibility that inhibitors against Cdk12 could be used as chemotherapeutics. Despite this growing clinical interest, the mechanism behind Cdk12's regulation of HR genes remains unknown. Here we show that Cdk12 suppresses intronic polyadenylation (IPA) and that this mechanism explains the exquisite sensitivity of HR genes to Cdk12 loss. We find that Cdk12 globally enhances transcription elongation rate to kinetically suppress IPA events. Many HR genes harbor multiple IPA sites per gene, and the cumulative effect of these sites accounts for the increased sensitivity of HR genes to Cdk12. Finally, we find evidence that Cdk12 LOF mutations and deletions cause upregulation of IPA sites in HR genes in human tumors. Our results define the mechanism by which Cdk12 regulates transcription, mRNA biogenesis, and the HR pathway. This work clarifies the biological function of CDK12 and underscores its potential both as a chemotherapeutic target and as a tumor biomarker.
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis. Vita.Includes bibliographical references.
DepartmentMassachusetts Institute of Technology. Department of Biology.
Massachusetts Institute of Technology