CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

Abstract

RNA splicing, the process of intron removal from pre-mRNA, is essential for the regulation of gene expression. It is controlled by the spliceosome, a megadalton RNA-protein complex that assembles de novo on each pre-mRNA intron via an ordered assembly of intermediate complexes 1,2 . Spliceosome activation is a major control step requiring dramatic protein and RNA rearrangements leading to a catalytically active complex [1][2][3][4][5] . Splicing factor 3B subunit 1 (SF3B1) protein, a subunit of the U2 snRNP 6 , is phosphorylated during spliceosome activation 7-10 , but the responsible kinase has not been identified. Here we show that cyclin-dependent kinase 11 (CDK11) associates with SF3B1 and phosphorylates threonine residues at its N-terminus during spliceosome activation. The phosphorylation is important for association of SF3B1 with U5 and U6 snRNAs in activated spliceosome, termed B act complex, and it can be blocked by OTS964, a potent and selective inhibitor of CDK11. CDK11 inhibition prevents spliceosomal transition from the precatalytic complex B to the activated complex B act and leads to widespread intron retention and accumulation of non-functional spliceosomes on pre-mRNAs and chromatin. We demonstrate a central role of CDK11 in spliceosome assembly and splicing regulation and characterize OTS964 as a highly selective CDK11 inhibitor that suppresses spliceosome activation and splicing.

P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway

“…Finally, we asked whether specific pharmacological targeting of other major tCDKs can also induce synthetic lethality in combination with Nutlin-3a. We targeted CDK7, CDK8, CDK11 and CDK12/13 using YKL-5–124 ( 56 ), Senexin A ( 57 ), OTS964 ( 16 , 58 ) and THZ531 ( 59 ) inhibitors, respectively, and conducted the combinatorial cytotoxicity and Bliss synergy score assays. While targeting CDK8 was not cytotoxic to HCT116 cells, inhibitors of other tCDKs showed modest cytotoxicity in the absence of Nutlin-3a.…”

“…Another set of well-studied tCDKs includes CDK8 and its CDK19 paralogue, which bind cyclin C to influence gene expression by phosphorylating transcription factors and controlling structure and function of the Mediator ( 14 ). Finally, CDK11 binds cyclins L1 and L2 to regulate transcription and pre-mRNA splicing by phosphorylating the CTD of Pol II and the U2 small nuclear ribonucleoprotein subunit SF3B1 ( 15 , 16 ).…”

SAP30BP interacts with RBM17/SPF45 to promote splicing in a subset of human short introns

“…Some data may help to address this question. Since previous in vitro spliceosome analyses showed that SF3B1 is phosphorylated during spliceosome activation, typically from B to B act complex (Wang et al, 1998; Shi et al, 2006; Bessonov et al, 2010; Agafonov et al, 2011; Hluchý et al, 2022), we paid attention to the phosphorylation status of SF3B1 that interacts with RBM17. Our in vitro binding assay revealed that RBM17 can bind to total SF3B1, but without SAP30BP, RBM17 does not bind well to active phosphorylated SF3B1.…”

Therapeutic potential of CDK11 in cancer

“…demonstrated that OTS964 blocks pre‐mRNA splicing in a similar manner to the splicing inhibitor pladienolide B, but via a different mechanism. 7 Pre‐mRNA splicing is performed by a spliceosome, a huge RNA‐protein complex that is progressively assembled on introns via spliceosome intermediate complexes termed E, A, B, B act , B*, C, C*. The intermediates are formed by the stepwise recruitment and release of small nuclear ribonucleoprotein particles (snRNPs) named U1, U2, U4, U5 and U6.…”