CDK11 phosphorylates SF3B1 and is essential for constitutive splicing (RNA-seq)

Pre-mRNA splicing is a highly regulated process catalyzing intron excision by spliceosome. Spliceosome activation is a major control step requiring dramatic protein and RNA rearrangements leading to a catalytically active complex. Prior research has linked hyperphosphorylation of SF3B1, a subunit of U2 snRNP, with spliceosome activation and catalytically active spliceosome, rendering a relevant kinase a key player for pre-mRNA splicing. Here we use OTS964, the first potent inhibitor of cyclin-dependent kinase 11 (CDK11), to show rapid and selective dephosphorylation of SF3B1 on threonines required for spliceosome activation. CDK11 associates with SF3B1 and its inhibition causes massive intron retention, block in precatalytic spliceosome complex B to activated spliceosome complex Bact transition and accumulation of non-functional spliceosomes on pre-mRNA and chromatin. These studies reveal crucial regulatory role of CDK11 in human pre-mRNA splicing and define the compound OTS964 as a quality chemical biology probe for CDK11. Examination of RNA-seq, 4SU-seq, SF3B1 iCLIP, U2AF65 iCLIP,AQR iCLIP,P-Ser2 ChI, P-Ser5 ChIP, P-Ser7 ChIP, and RNAPolII ChIP in the presence or absence of OTS964 inhibitor on HCT116 cells