CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

• Published in: Nature (London) Vol. 609; no. 7928; pp. 829 - 834
• Main Authors: Hluchý, Milan, Gajdušková, Pavla, Ruiz de los Mozos, Igor, Rájecký, Michal, Kluge, Michael, Berger, Benedict-Tilman, Slabá, Zuzana, Potěšil, David, Weiß, Elena, Ule, Jernej, Zdráhal, Zbyněk, Knapp, Stefan, Paruch, Kamil, Friedel, Caroline C., Blazek, Dalibor
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.09.2022; Nature Publishing Group
• Subjects: 13; 13/1; 13/106; 38/15; 38/77; 38/91; 631/337/1645/1792; 631/337/572; 631/67; 631/92/275; 96; Assembly; Chromatin; Chromatin - metabolism; Cyclin-dependent kinase; Cyclin-dependent kinases; Cyclin-Dependent Kinases - antagonists & inhibitors; Cyclin-Dependent Kinases - metabolism; Enzyme Activation - drug effects; Gene expression; Humanities and Social Sciences; Kinases; multidisciplinary; Phosphoproteins - chemistry; Phosphoproteins - metabolism; Phosphorylation; Proteins; Quinolones - pharmacology; Ratios; Recruitment; Retention; Ribonucleic acid; Ribonucleoprotein, U2 Small Nuclear - chemistry; Ribonucleoprotein, U2 Small Nuclear - metabolism; RNA; RNA polymerase; RNA Precursors - genetics; RNA Precursors - metabolism; RNA Splicing - drug effects; Science; Science (multidisciplinary); Spliceosomes; Spliceosomes - drug effects; Spliceosomes - metabolism; Splicing; Splicing factors; Threonine; Threonine - metabolism
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-022-05204-z

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 ribonucleoprotein 6 —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. CDK11 associates with SF3B1 and phosphorylates threonine residues at the N terminus of SF3B1 during spliceosome activation, and the inhibition of CDK11 blocks the activation and leads to widespread intron retention and the accumulation of non-functional spliceosomes on pre-mRNAs and chromatin.