CDK7 regulates pre-mRNA splicing via CDK11

Cyclin-dependent kinase 11 (CDK11) is essential for the regulation of pre-mRNA splicing by phosphorylating SF3B1, a core spliceosome component. This phosphorylation is a marker of the catalytically active spliceosome, so it is important to identify the mechanisms that regulate CDK11. Herein, we report that a small subset of CDK11 is phosphorylated on the activation T-loop threonine 595 (Thr595) and is associated with the activated spliceosome on chromatin in gene bodies. Mutational analyses revealed that Thr595 is essential for the formation of the active CDK11 complex with cyclin L and SAP30BP. CDK11 transiently associates with CDK7, a transcriptional kinase that also promotes the activation of other CDKs. The time course of the inhibition of CDK7 initially decreases transcription, but later produces unspliced pre-mRNAs. The dynamics of onset of the CDK7-mediated splicing defect correlates with the sequential dephosphorylation of CDK11 Thr595 and SF3B1. SILAC-based phospho-proteomics upon brief CDK11 inhibition identified SF3B1, CDC5L and ESS2 as CDK11 substrates, an overlap with the previously identified CDK7 substrates in the spliceosome. In summary, our study suggests that CDK7 likely acts via CDK11 Thr595 phosphorylation to regulate pre-mRNA splicing in cells. The identification of additional CDK11 substrates indicates its more complex role in spliceosome regulation.