CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

Milan Hluchý; Pavla Gajdušková; Igor Ruiz de los Mozos; Michal Rájecký; Michael Kluge; Benedict Tilman Berger; Zuzana Slabá; David Potěšil; Elena Weiß; Jernej Ule; Zbyněk Zdráhal; Stefan Knapp; Kamil Paruch; Caroline C. Friedel; Dalibor Blazek

doi:10.1038/s41586-022-05204-z

CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

Milan Hluchý, Pavla Gajdušková, Igor Ruiz de los Mozos, Michal Rájecký, Michael Kluge, Benedict Tilman Berger, Zuzana Slabá, David Potěšil, Elena Weiß, Jernej Ule, Zbyněk Zdráhal, Stefan Knapp, Kamil Paruch, Caroline C. Friedel, Dalibor Blazek^*

^*Corresponding author for this work

Basic and Clinical Neuroscience

Research output: Contribution to journal › Article › peer-review

30 Citations (Scopus)

287 Downloads (Pure)

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.

Original language	English
Pages (from-to)	829-834
Number of pages	6
Journal	Nature
Volume	609
Issue number	7928
Early online date	14 Sept 2022
DOIs	https://doi.org/10.1038/s41586-022-05204-z
Publication status	Published - 22 Sept 2022

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/s41586-022-05204-z

CDK11 regulates pre-mRNA_HLUCHY_Publishedonline14September2022_GREEN AAMAccepted author manuscript, 5.34 MB

Cite this

@article{d76536db78424306a949a4bd0ed14dda,

title = "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 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.",

author = "Milan Hluch{\'y} and Pavla Gajdu{\v s}kov{\'a} and {Ruiz de los Mozos}, Igor and Michal R{\'a}jeck{\'y} and Michael Kluge and Berger, {Benedict Tilman} and Zuzana Slab{\'a} and David Pot{\v e}{\v s}il and Elena Wei{\ss} and Jernej Ule and Zbyn{\v e}k Zdr{\'a}hal and Stefan Knapp and Kamil Paruch and Friedel, {Caroline C.} and Dalibor Blazek",

note = "Funding Information: We thank all of the members of the Blazek laboratory for discussions throughout the project and comments on the manuscript; M. Hallegger for protocols and advice regarding in vitro splicing assays; M. {\v S}ebesta for providing GST–RNAPII, T. B{\'a}rta for providing anti-CDK2 antibodies; K. Han{\'a}kov{\'a} for assistance with proteomic experiments; and the staff at Life Science Editors for editing services. This research was supported by grants from the Czech Science Foundation (21-19266S); the CEITEC (Project CEITEC-Central-European Institute of Technology (CZ.1.05/1.1.00/02.0068)); GAMU MUNI/G/1129/2021 to D.B.; the Deutsche Forschungsgemeinschaft (DFG; grants FR2938/9-1 and FR2938/10-1) to C.C.F.; the European Union{\textquoteright}s Horizon 2020 research and innovation programme (835300-RNPdynamics) to J.U; European Structural and Investment Funds, Operational Programme Research, Development and Education—“Preclinical Progression of New Organic Compounds with Targeted Biological Activity” (Preclinprogress)—CZ.02.1.01/0.0/0.0/16_025/0007381, project no. LQ1605 from the National Program of Sustainability II (MEYS CR); the project CZ-OPENSCREEN: National Infrastructure for Chemical Biology (LM2018130); Bader Philanthropies; and GAMU MUNI/G/1129/2021 to K.P. CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2018127, is acknowledged for the financial support of the measurements at the CEITEC Proteomics Core Facility. Computational resources were supplied by the project “e-Infrastruktura CZ” (e-INFRA CZ ID: 90140) supported by the Ministry of Education, Youth and Sports of the Czech Republic. S.K. and B.-T.B. are grateful for support from the SGC, a registered charity (no. 1097737) that receives funds from AbbVie, Bayer, Boehringer Ingelheim, the Canada Foundation for Innovation, Eshelman Institute for Innovation, Genentech, Genome Canada through Ontario Genomics Institute (OGI-196), EU/EFPIA/OICR/McGill/KTH/Diamond, Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN grant 875510), Janssen, Merck, Merck & Co, Pfizer, Takeda and Wellcome; S.K. from the German translational cancer network (DKTK) and the Frankfurt Cancer Institute (FCI); and S.K. and B.-T.B. from the collaborative research center 1399 “Mechanisms of drug sensitivity and resistance in small cell lung cancer”. CTD Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive licence to Springer Nature Limited.",

year = "2022",

month = sep,

day = "22",

doi = "10.1038/s41586-022-05204-z",

language = "English",

volume = "609",

pages = "829--834",

journal = "Nature",

issn = "0028-0836",

publisher = "Springer Nature",

number = "7928",

}

TY - JOUR

T1 - CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

AU - Hluchý, Milan

AU - Gajdušková, Pavla

AU - Ruiz de los Mozos, Igor

AU - Rájecký, Michal

AU - Kluge, Michael

AU - Berger, Benedict Tilman

AU - Slabá, Zuzana

AU - Potěšil, David

AU - Weiß, Elena

AU - Ule, Jernej

AU - Zdráhal, Zbyněk

AU - Knapp, Stefan

AU - Paruch, Kamil

AU - Friedel, Caroline C.

AU - Blazek, Dalibor

N1 - Funding Information: We thank all of the members of the Blazek laboratory for discussions throughout the project and comments on the manuscript; M. Hallegger for protocols and advice regarding in vitro splicing assays; M. Šebesta for providing GST–RNAPII, T. Bárta for providing anti-CDK2 antibodies; K. Hanáková for assistance with proteomic experiments; and the staff at Life Science Editors for editing services. This research was supported by grants from the Czech Science Foundation (21-19266S); the CEITEC (Project CEITEC-Central-European Institute of Technology (CZ.1.05/1.1.00/02.0068)); GAMU MUNI/G/1129/2021 to D.B.; the Deutsche Forschungsgemeinschaft (DFG; grants FR2938/9-1 and FR2938/10-1) to C.C.F.; the European Union’s Horizon 2020 research and innovation programme (835300-RNPdynamics) to J.U; European Structural and Investment Funds, Operational Programme Research, Development and Education—“Preclinical Progression of New Organic Compounds with Targeted Biological Activity” (Preclinprogress)—CZ.02.1.01/0.0/0.0/16_025/0007381, project no. LQ1605 from the National Program of Sustainability II (MEYS CR); the project CZ-OPENSCREEN: National Infrastructure for Chemical Biology (LM2018130); Bader Philanthropies; and GAMU MUNI/G/1129/2021 to K.P. CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2018127, is acknowledged for the financial support of the measurements at the CEITEC Proteomics Core Facility. Computational resources were supplied by the project “e-Infrastruktura CZ” (e-INFRA CZ ID: 90140) supported by the Ministry of Education, Youth and Sports of the Czech Republic. S.K. and B.-T.B. are grateful for support from the SGC, a registered charity (no. 1097737) that receives funds from AbbVie, Bayer, Boehringer Ingelheim, the Canada Foundation for Innovation, Eshelman Institute for Innovation, Genentech, Genome Canada through Ontario Genomics Institute (OGI-196), EU/EFPIA/OICR/McGill/KTH/Diamond, Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN grant 875510), Janssen, Merck, Merck & Co, Pfizer, Takeda and Wellcome; S.K. from the German translational cancer network (DKTK) and the Frankfurt Cancer Institute (FCI); and S.K. and B.-T.B. from the collaborative research center 1399 “Mechanisms of drug sensitivity and resistance in small cell lung cancer”. CTD Publisher Copyright: © 2022, The Author(s), under exclusive licence to Springer Nature Limited.

PY - 2022/9/22

Y1 - 2022/9/22

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85138212060&partnerID=8YFLogxK

U2 - 10.1038/s41586-022-05204-z

DO - 10.1038/s41586-022-05204-z

M3 - Article

C2 - 36104565

AN - SCOPUS:85138212060

SN - 0028-0836

VL - 609

SP - 829

EP - 834

JO - Nature

JF - Nature

IS - 7928

ER -

CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

Abstract

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this