Interaction of Cyclin-Dependent Kinase 12/CrkRS with Cyclin K1 Is Required for the Phosphorylation of the C-Terminal Domain of RNA Polymerase II

Abstract

e CrkRS (Cdc2-related kinase, Arg/Ser), or cyclin-dependent kinase 12 (CKD12), is a serine/threonine kinase believed to coordinate transcription and RNA splicing. While CDK12/CrkRS complexes were known to phosphorylate the C-terminal domain (CTD) of RNA polymerase II (RNA Pol II), the cyclin regulating this activity was not known. Using immunoprecipitation and mass spectrometry, we identified a 65-kDa isoform of cyclin K (cyclin K1) in endogenous CDK12/CrkRS protein complexes. We show that cyclin K1 complexes isolated from mammalian cells contain CDK12/CrkRS but do not contain CDK9, a presumed partner of cyclin K. Analysis of extensive RNA-Seq data shows that the 65-kDa cyclin K1 isoform is the predominantly expressed form across numerous tissue types. We also demonstrate that CDK12/CrkRS is dependent on cyclin K1 for its kinase activity and that small interfering RNA (siRNA) knockdown of CDK12/CrkRS or cyclin K1 has similar effects on the expression of a luciferase reporter gene. Our data suggest that cyclin K1 is the primary cyclin partner for CDK12/CrkRS and that cyclin K1 is required to activate CDK12/CrkRS to phosphorylate the CTD of RNA Pol II. These properties are consistent with a role of CDK12/CrkRS in regulating gene expression through phosphorylation of RNA Pol II.

Heterochromatin remodeling by CDK12 contributes to learning in Drosophila

“…S1G). In addition, we found that depletion of cyclin K (CycK), a known functional partner of CDK12 (13)(14)(15), induced heterochromatin enrichment on the chromosomes (Fig. S2 A and B), supporting that CDK12 is involved in counteracting heterochromatin enrichment.…”

“…Neverthless, emerging evidence has shown that CDK12 contains the arginine/serine domain and is involved in RNA processing (32,33). In addition, CDK12 has been implicated in mRNA splicing (15,34,35). However, from our data, we cannot exclude the possibility that the arginine/serine domain of CDK12 also contributes to heterochromatin remodeling.…”

Cdks, cyclins and CKIs: roles beyond cell cycle regulation

“…3), newly annotated members of the Cdk and cyclin families continue to join the ranks in the control of RNA Pol II-based transcription. Specifically, it was recently demonstrated that cyclin K partners with Cdk12 and Cdk13 to mediate phosphorylation of the CTD (Bartkowiak et al, 2010;Blazek et al, 2011;Cheng et al, 2012). Collectively, it should be appreciated that the control of RNA Pol II-based transcription is analogous to the regulation of the cell cycle, whereby a series of Cdk/cyclin complexes, activities of which are restricted during each phase of the transcription cycle, is required to achieve the dynamic patterns of phosphorylation marks on the CTD and drive the step-wise progression from pre-initiation, initiation, elongation to termination (Fig.…”

Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications

“…Effect of CDK12 knockdown in cellular models has been consistently associated with HRD (3,5,7,8). HRD in breast and ovarian cancers is mostly related to BRCA1/2 inactivation (9-11).…”

“…CDK12 attracted particular attention as cells inactivated for the CDK12 display hypersensitivity to DNA-damaging agents and to PARP1/2 inhibitors (5,6). This effect of CDK12 inactivation was associated with homologous recombination (HR) deficiency (HRD) due to decreased expression observed for some HR genes, such as BRCA1, FANCI, or FANCD2 (3,5,7,8). HRD due to inactivation of BRCA1 or BRCA2, the two major genes implicated in ovarian cancer, leads to the large-scale chromosomal instability, readily observed in nearly half of HGS-OvCa (9)(10)(11).…”