PAF1C allosterically activates CDK12/13 kinase during RNAPII transcript elongation

The mechanisms ensuring temporally correct, site-specific phosphorylation of the RNA polymerase II C-terminal domain (CTD) by cyclin-dependent kinases (CDKs) during the transcription cycle remain poorly understood. Here, we present results from in vitro reconstitution of CTD phosphorylation combined with in vivo evidence to show that human CDK12 and CDK9 both co-phosphorylate CTD Serine 5 and Serine 2. However, only phosphorylation by CDK12 is stimulated by association with the elongation-specific factor PAF1C, in which the CDC73 subunit contains a short, conserved motif capable of association with and activation of CDK12/Cyclin K. This motif is necessary for cell proliferation and crucial for CTD phosphorylation and transcript elongation. Together, these data provide new insight into basic mechanisms ensuring CDK specificity in the RNAPII transcription cycle.