Milan Hluchý  ^# 1,  Pavla Gajdušková  ^# 1,  Igor Ruiz de Los Mozos ^2 3 4,  Michal Rájecký ¹,  Michael Kluge ⁵,  Benedict-Tilman Berger ^6 7,  Zuzana Slabá ¹,  David Potěšil ¹,  Elena Weiß ⁵,  Jernej Ule ^2 8,  Zbyněk Zdráhal ¹,  Stefan Knapp ^6 7,  Kamil Paruch ^9 10,  Caroline C Friedel ⁵,  Dalibor Blazek ¹¹

Affiliations

• 1Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
• 2The Francis Crick Institute, London, UK.
• 3Department of Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain.
• 4Center for Applied Medical Research, University of Navarra, Pamplona, Spain.
• 5Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany.
• 6Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
• 7Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
• 8UK Dementia Research Institute, King's College London, London, UK.
• 9Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
• 10International Clinical Research Center, St Anne's University Hospital in Brno, Brno, Czech Republic.
• 11Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic. dalibor.blazek@ceitec.muni.cz.
• #Contributed equally.

PMID: 36104565    DOI: 10.1038/s41586-022-05204-z

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 through an ordered assembly of intermediate complexes^1,2. Spliceosome activation is a major control step that requires substantial protein and RNA rearrangements leading to a catalytically active complex^1-5. Splicing factor 3B subunit 1 (SF3B1) protein-a subunit of the U2 small nuclear ribonucleoprotein⁶-is phosphorylated during spliceosome activation^7-10, 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 B^act 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 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.