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 through an ordered assembly of intermediate complexes1,2. Spliceosome activation is a major control step that requires substantial protein and RNA rearrangements leading to a catalytically active complex1-5. Splicing factor 3B subunit 1 (SF3B1) protein-a subunit of the U2 small nuclear ribonucleoprotein6-is phosphorylated during spliceosome activation7-10, but the kinase that is responsible 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 the association between SF3B1 and U5 and U6 snRNAs in the activated spliceosome, termed the Bact complex, and the phosphorylation can be blocked by OTS964, a potent and selective inhibitor of CDK11. Inhibition of CDK11 prevents spliceosomal transition from the precatalytic complex B to the activated complex Bact 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.

Center for Applied Medical Research University of Navarra Pamplona Spain

Central European Institute of Technology Masaryk University Brno Czech Republic

Department of Chemistry Faculty of Science Masaryk University Brno Czech Republic

Department of Personalized Medicine NASERTIC Government of Navarra Pamplona Spain

Institut für Informatik Ludwig Maximilians Universität München München Germany

Institut für Pharmazeutische Chemie Goethe University Frankfurt am Main Frankfurt am Main Germany

International Clinical Research Center St Anne's University Hospital in Brno Brno Czech Republic

Structural Genomics Consortium Goethe University Frankfurt am Main Frankfurt am Main Germany

The Francis Crick Institute London UK

UK Dementia Research Institute King's College London London UK

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Clin Transl Med. 2023 Mar;13(3):e1201. doi: 10.1002/ctm2.1201. PubMed

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Therapeutic potential of CDK11 in cancer