Abstract
Splicing Factor 3b Subunit 1 (SF3B1), a core component of the spliceosome, undergoes dynamic phosphorylation and dephosphorylation during the splicing cycle to regulate pre-mRNA splicing. Twenty-eight threonine/proline repeats are phosphorylated by CDK11 during spliceosome activation and remain phosphorylated in the catalytically active spliceosomes. The function of phosphorylated SF3B1 (P-SF3B1), and the identity of spliceosomes stalled by CDK11 inhibition remain unclear. Using quantitative proteomics of chromatin-associated spliceosomes, we identify a previously uncharacterized intermediate complex BOTS964, arrested by CDK11 inhibitor OTS964, that incorporates the nineteen-related (NTR) but not nineteen (NTC) complex. iCLIP-seq revealed that P-SF3B1 engages with the U6 snRNA internal stem-loop (ISL), suggesting a potential role in stabilizing the RNA catalytic core. We further demonstrate that P-SF3B1 is recognized by forkhead-associated (FHA) domain of SNIP1, which promotes recruitment of retention and splicing (RES) complex during spliceosome activation. Acute SNIP1 depletion disrupts RES incorporation, causes widespread splicing defects, and promotes hyperphosphorylation of SF3B1 by CDK11. Mutations in SNIP1 FHA domain, including the neurodevelopmental disorder-associated E366G variant, impair P-SF3B1 binding, pre-mRNA splicing, and cell viability. Together, these findings uncover the phosphorylation-dependent CDK11/P-SF3B1/SNIP1 signaling axis that is critical for pre-mRNA splicing and cellular proliferation and provide a mechanistic insight into its dysregulation in disease.
Similar content being viewed by others
Data availability
All next-generation-sequencing raw and processed data are available at the NCBI’s Gene Expression Omnibus under the GEO series accession numbers GSE295433 (iCLIP-seq) and GSE295435 (RNA-seq). All proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063160 and PXD063162. Source data are provided with this paper.
References
Carrocci, T. J. & Neugebauer, K. M. Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing. Mol. Cell 84, 3656–3666 (2024).
Kastner, B., Will, C.L., Stark, H. & Luhrmann, R. Structural insights into nuclear pre-mRNA splicing in higher eukaryotes. Cold Spring Harb Perspect Biol. 11, a032417 (2019).
Wan, R., Bai, R., Zhan, X. & Shi, Y. How is precursor messenger RNA spliced by the spliceosome? Annu Rev. Biochem. 89, 333–358 (2020).
Wilkinson, M. E., Charenton, C. & Nagai, K. RNA splicing by the spliceosome. Annu Rev. Biochem. 89, 359–388 (2020).
Shenasa, H. & Bentley, D. L. Pre-mRNA splicing and its cotranscriptional connections. Trends Genet. 39, 672–685 (2023).
Rogalska, M. E., Vivori, C. & Valcarcel, J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat. Rev. Genet. 24, 251–269 (2023).
Schneider, M. et al. Human PRP4 kinase is required for stable tri-snRNP association during spliceosomal B complex formation. Nat. Struct. Mol. Biol. 17, 216–221 (2010).
Hluchy, M. et al. CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1. Nature 609, 829–834 (2022).
Mathew, R. et al. Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. Nat. Struct. Mol. Biol. 15, 435–443 (2008).
Makarov, E. M. et al. Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome. Science 298, 2205–2208 (2002).
Bessonov, S. et al. Characterization of purified human Bact spliceosomal complexes reveals compositional and morphological changes during spliceosome activation and first step catalysis. RNA 16, 2384–2403 (2010).
Townsend, C. et al. Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Science 370, eabc3753(2020).
Zhang, X. et al. Structure of the human activated spliceosome in three conformational states. Cell Res. 28, 307–322 (2018).
Boesler, C. et al. A spliceosome intermediate with loosely associated tri-snRNP accumulates in the absence of Prp28 ATPase activity. Nat. Commun. 7, 11997 (2016).
Zhang, Z. et al. Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. EMBO J. 43, 1065–1088 (2024).
Zhan, X., Lu, Y. & Shi, Y. Molecular basis for the activation of human spliceosome. Nat. Commun. 15, 6348 (2024).
Fabrizio, P. et al. The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome. Mol. Cell 36, 593–608 (2009).
Hoskins, A.A., Rodgers, M.L., Friedman, L.J., Gelles, J. & Moore, M.J. Single molecule analysis reveals reversible and irreversible steps during spliceosome activation. Elife 5, e14166(2016).
Chan, S. P., Kao, D. I., Tsai, W. Y. & Cheng, S. C. The Prp19p-associated complex in spliceosome activation. Science 302, 279–282 (2003).
Hluchy, M. & Blazek, D. CDK11, a splicing-associated kinase regulating gene expression. Trends Cell Biol. 35, 702–716 (2024).
Sun, C. The SF3b complex: splicing and beyond. Cell Mol. Life Sci. 77, 3583–3595 (2020).
Kotake, Y. et al. Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat. Chem. Biol. 3, 570–575 (2007).
Cretu, C. et al. Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Mol. Cell 70, 265–273 e8 (2018).
Teng, T. et al. Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A-SF3b complex. Nat. Commun. 8, 15522 (2017).
Seiler, M. et al. H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers. Nat. Med. 24, 497–w504 (2018).
Corrionero, A., Minana, B. & Valcarcel, J. Reduced fidelity of branch point recognition and alternative splicing induced by the anti-tumor drug spliceostatin A. Genes Dev. 25, 445–459 (2011).
Girard, C. et al. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nat. Commun. 3, 994 (2012).
Wang, C. et al. Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis. Genes Dev. 12, 1409–1414 (1998).
Vieira-Vieira, C. H., Dauksaite, V., Sporbert, A., Gotthardt, M. & Selbach, M. Proteome-wide quantitative RNA-interactome capture identifies phosphorylation sites with regulatory potential in RBM20. Mol. Cell 82, 2069–2083 e8 (2022).
Cass, D. M. & Berglund, J. A. The SF3b155 N-terminal domain is a scaffold important for splicing. Biochemistry 45, 10092–10101 (2006).
Galardi, J. W. et al. A UHM-ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing. J. Biol. Chem. 298, 102224 (2022).
Murthy, T. et al. Cyclin-dependent kinase 1 (CDK1) and CDK2 have opposing roles in regulating interactions of splicing factor 3B1 with chromatin. J. Biol. Chem. 293, 10220–10234 (2018).
Corsini, L. et al. Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60. J. Biol. Chem. 284, 630–639 (2009).
Fukumura, K. et al. SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns. Nat. Commun. 12, 4910 (2021).
Loerch, S. & Kielkopf, C. L. Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. RNA 22, 1795–1807 (2016).
Tari, M. et al. U2AF(65) assemblies drive sequence-specific splice site recognition. EMBO Rep. 20, e47604 (2019).
Brewer, A. et al. Mapping the substrate landscape of protein phosphatase 2A catalytic subunit PPP2CA. iScience 27, 109302 (2024).
Shi, Y., Reddy, B. & Manley, J. L. PP1/PP2A phosphatases are required for the second step of Pre-mRNA splicing and target specific snRNP proteins. Mol. Cell 23, 819–829 (2006).
Dziembowski, A. et al. Proteomic analysis identifies a new complex required for nuclear pre-mRNA retention and splicing. EMBO J. 23, 4847–4856 (2004).
Wysoczanski, P. et al. Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex. Nat. Struct. Mol. Biol. 21, 911–918 (2014).
Bao, P., Will, C. L., Urlaub, H., Boon, K. L. & Luhrmann, R. The RES complex is required for efficient transformation of the precatalytic B spliceosome into an activated B(act) complex. Genes Dev. 31, 2416–2429 (2017).
Frankiw, L. et al. BUD13 promotes a type I interferon response by countering intron retention in Irf7. Mol. Cell 73, 803–814 e6 (2019).
Fernandez, J. P. et al. RES complex is associated with intron definition and required for zebrafish early embryogenesis. PLoS Genet. 14, e1007473 (2018).
Durocher, D. & Jackson, S. P. The FHA domain. FEBS Lett. 513, 58–66 (2002).
Durocher, D. et al. The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms. Mol. Cell 6, 1169–1182 (2000).
Meng, D. et al. A molecular brake that modulates spliceosome pausing at detained introns contributes to neurodegeneration. Protein Cell 14, 318–336 (2023).
Ammous, Z. et al. A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder. PLoS Genet. 17, e1009803 (2021).
Puffenberger, E. G. et al. Genetic mapping and exome sequencing identify variants associated with five novel diseases. PLoS One 7, e28936 (2012).
Matsui, Y. et al. SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development. Nat. Commun. 14, 4754 (2023).
Roche, K. C., Rocha, S., Bracken, C. P. & Perkins, N. D. Regulation of ATR-dependent pathways by the FHA domain containing protein SNIP1. Oncogene 26, 4523–4530 (2007).
Kim, R. H. et al. A novel smad nuclear interacting protein, SNIP1, suppresses p300-dependent TGF-beta signal transduction. Genes Dev. 14, 1605–1616 (2000).
Fujii, M. et al. SNIP1 is a candidate modifier of the transcriptional activity of c-Myc on E box-dependent target genes. Mol. Cell 24, 771–783 (2006).
Yu, B. et al. KMT5A-methylated SNIP1 promotes triple-negative breast cancer metastasis by activating YAP signaling. Nat. Commun. 13, 2192 (2022).
Bracken, C. P. et al. Regulation of cyclin D1 RNA stability by SNIP1. Cancer Res. 68, 7621–7628 (2008).
Chen, L. L. et al. SNIP1 recruits TET2 to regulate c-MYC target genes and cellular DNA damage response. Cell Rep. 25, 1485–1500.e4 (2018).
Kfir, N. et al. SF3B1 association with chromatin determines splicing outcomes. Cell Rep. 11, 618–629 (2015).
Boddu, P. C. et al. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Mol. Cell 84, 1475–1495 (2024).
Caizzi, L. et al. Efficient RNA polymerase II pause release requires U2 snRNP function. Mol. Cell 81, 1920–1934.e9 (2021).
Tresini, M. et al. The core spliceosome as target and effector of non-canonical ATM signalling. Nature 523, 53–58 (2015).
Nojima, T., Gomes, T., Carmo-Fonseca, M. & Proudfoot, N. J. Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide. Nat. Protoc. 11, 413–428 (2016).
Konig, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909–915 (2010).
Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274–287 (2014).
Fica, S. M., Mefford, M. A., Piccirilli, J. A. & Staley, J. P. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat. Struct. Mol. Biol. 21, 464–471 (2014).
Toor, N., Keating, K. S., Taylor, S. D. & Pyle, A. M. Crystal structure of a self-spliced group II intron. Science 320, 77–82 (2008).
Galej, W. P. et al. Cryo-EM structure of the spliceosome immediately after branching. Nature 537, 197–201 (2016).
Wan, R., Yan, C., Bai, R., Huang, G. & Shi, Y. Structure of a yeast catalytic step I spliceosome at 3.4 A resolution. Science 353, 895–904 (2016).
Boudrez, A., Beullens, M., Waelkens, E., Stalmans, W. & Bollen, M. Phosphorylation-dependent interaction between the splicing factors SAP155 and NIPP1. J. Biol. Chem. 277, 31834–31841 (2002).
Tanuma, N. et al. Nuclear inhibitor of protein phosphatase-1 (NIPP1) directs protein phosphatase-1 (PP1) to dephosphorylate the U2 small nuclear ribonucleoprotein particle (snRNP) component, spliceosome-associated protein 155 (Sap155). J. Biol. Chem. 283, 35805–35814 (2008).
Loyer, P. et al. Characterization of cyclin L1 and L2 interactions with CDK11 and splicing factors: influence of cyclin L isoforms on splice site selection. J. Biol. Chem. 283, 7721–7732 (2008).
Wang, C. et al. CDK11 requires a critical activator SAP30BP to regulate pre-mRNA splicing. EMBO J. 42, e114051 (2023).
Nabet, B. et al. The dTAG system for immediate and target-specific protein degradation. Nat. Chem. Biol. 14, 431–441 (2018).
Tellier, M., Maudlin, I. & Murphy, S. Transcription and splicing: a two-way street. Wiley Interdiscip. Rev. RNA 11, e1593 (2020).
Caizzi, L. et al. Efficient RNA polymerase II pause release requires U2 snRNP function. Mol. Cell 81, 1920–1934 (2021).
Devlin, J. R. et al. A CDK11-dependent RNA polymerase II pause-checkpoint precedes CDK9-mediated transition to transcriptional elongation. Mol. Cell 85, 3256–3274.e14 (2025).
Rimel, J.K. et al. Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription. Genes Dev. 34, 1452–1473 (2020).
Sanso, M. et al. P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates. Genes Dev. 30, 117–131 (2016).
Tellier, M. et al. CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation. EMBO Rep. 23, e54520 (2022).
Krajewska, M. et al. CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation. Nat. Commun. 10, 1757 (2019).
Panzeri, V., Pieraccioli, M., Cesari, E., de la Grange, P. & Sette, C. CDK12/13 promote splicing of proximal introns by enhancing the interaction between RNA polymerase II and the splicing factor SF3B1. Nucleic Acids Res 51, 5512–5526 (2023).
Olson, C. M. et al. Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation. Nat. Chem. Biol. 14, 163–170 (2018).
Zhang, T. et al. Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors. Nat. Chem. Biol. 12, 876–884 (2016).
Larochelle, S. et al. Dichotomous but stringent substrate selection by the dual-function Cdk7 complex revealed by chemical genetics. Nat. Struct. Mol. Biol. 13, 55–62 (2006).
Rajecky, M. et al. CDK7-CDK11 axis in spliceosome regulation and pre-mRNA splicing. Nucleic Acids Res. 53, gkaf1343 (2025).
Kim, M., Suh, H., Cho, E. J. & Buratowski, S. Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J. Biol. Chem. 284, 26421–26426 (2009).
Glover-Cutter, K. et al. TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II. Mol. Cell Biol. 29, 5455–5464 (2009).
Akhtar, M. S. et al. TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol. Cell 34, 387–393 (2009).
AJ, C. Q., Bugai, A. & Barboric, M. Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb. Nucleic Acids Res. 44, 7527–7539 (2016).
Parua, P. K., Kalan, S., Benjamin, B., Sanso, M. & Fisher, R. P. Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II. Nat. Commun. 11, 4338 (2020).
Chirackal Manavalan, A. P. et al. CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes. EMBO Rep. 20, e47592 (2019).
Pilarova, K., Herudek, J. & Blazek, D. CDK12: cellular functions and therapeutic potential of versatile player in cancer. NAR Cancer 2, zcaa003 (2020).
Fan, Z. et al. CDK13 cooperates with CDK12 to control global RNA polymerase II processivity. Sci. Adv. 6, eaaz5041(2020).
Bosken, C. A. et al. The structure and substrate specificity of human Cdk12/Cyclin K. Nat. Commun. 5, 3505 (2014).
Tellier, M. et al. CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation. Nucleic Acids Res. 48, 7712–7727 (2020).
Lopez Martinez, D. et al. PAF1C-mediated activation of CDK12/13 kinase activity is critical for CTD phosphorylation and transcript elongation. Mol. Cell 85, 1952–1967.e8 (2025).
Bartkowiak, B., Yan, C. & Greenleaf, A. L. Engineering an analog-sensitive CDK12 cell line using CRISPR/Cas. Biochim Biophys. Acta 1849, 1179–1187 (2015).
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Kuhn, A. N., van Santen, M. A., Schwienhorst, A., Urlaub, H. & Luhrmann, R. Stalling of spliceosome assembly at distinct stages by small-molecule inhibitors of protein acetylation and deacetylation. RNA 15, 153–175 (2009).
Agafonov, D. E. et al. ATPgammaS stalls splicing after B complex formation but prior to spliceosome activation. RNA 22, 1329–1337 (2016).
Sidarovich, A. et al. Identification of a small molecule inhibitor that stalls splicing at an early step of spliceosome activation. Elife 6, e23533(2017).
Fica, S. M. et al. RNA catalyses nuclear pre-mRNA splicing. Nature 503, 229–234 (2013).
Galej, W. P., Oubridge, C., Newman, A. J. & Nagai, K. Crystal structure of Prp8 reveals active site cavity of the spliceosome. Nature 493, 638–643 (2013).
Rasche, N. et al. Cwc2 and its human homologue RBM22 promote an active conformation of the spliceosome catalytic centre. EMBO J. 31, 1591–1604 (2012).
Weirich, S. & Jeltsch, A. Limited choice of natural amino acids as mimetics restricts design of protein lysine methylation studies. Nat. Commun. 14, 4097 (2023).
Lin, A. et al. Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. Sci. Transl. Med. 11, eaaw8412 (2019).
Blazek, D. Therapeutic potential of CDK11 in cancer. Clin. Transl. Med. 13, e1201 (2023).
Loyer, P. & Trembley, J. H. Roles of CDK/Cyclin complexes in transcription and pre-mRNA splicing: Cyclins L and CDK11 at the cross-roads of cell cycle and regulation of gene expression. Semin Cell Dev. Biol. 107, 36–45 (2020).
Zhou, Y., Shen, J. K., Hornicek, F. J., Kan, Q. & Duan, Z. The emerging roles and therapeutic potential of cyclin-dependent kinase 11 (CDK11) in human cancer. Oncotarget 7, 40846–40859 (2016).
Julian, L. et al. On-target toxicity limits the efficacy of CDK11 inhibition against cancers with 1p36 deletions. bioRxiv https://doi.org/10.1101/2025.08.03.668359 (2025).
Hsu, T. Y. et al. The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature 525, 384–388 (2015).
Kim, R. H. et al. SNIP1 inhibits NF-kappa B signaling by competing for its binding to the C/H1 domain of CBP/p300 transcriptional co-activators. J. Biol. Chem. 276, 46297–46304 (2001).
Roche, K. C., Wiechens, N., Owen-Hughes, T. & Perkins, N. D. The FHA domain protein SNIP1 is a regulator of the cell cycle and cyclin D1 expression. Oncogene 23, 8185–8195 (2004).
Cui, H. et al. The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-beta signaling. Nat. Commun. 13, 4680 (2022).
Chen, Y., Guo, W., Guo, X., Wanqing, Q. & Yin, Z. The clinical utilization of SNIP1 and its pathophysiological mechanisms in disease. Heliyon 10, e24601 (2024).
An, M. & Henion, P. D. The zebrafish sf3b1b460 mutant reveals differential requirements for the sf3b1 pre-mRNA processing gene during neural crest development. Int J. Dev. Biol. 56, 223–237 (2012).
Wang, Q., Moore, M. J., Adelmant, G., Marto, J. A. & Silver, P. A. PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. Genes Dev. 27, 615–626 (2013).
Reinhardt, H. C. & Yaffe, M. B. Phospho-Ser/Thr-binding domains: navigating the cell cycle and DNA damage response. Nat. Rev. Mol. Cell Biol. 14, 563–580 (2013).
Brooks, M. A. et al. Structure of the yeast Pml1 splicing factor and its integration into the RES complex. Nucleic Acids Res. 37, 129–143 (2009).
Wysoczanski, P. & Zweckstetter, M. Retention and splicing complex (RES) - the importance of cooperativity. RNA Biol. 13, 128–133 (2016).
Sakuma, T., Nakade, S., Sakane, Y., Suzuki, K. T. & Yamamoto, T. MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems. Nat. Protoc. 11, 118–133 (2016).
Brand, M. & Winter, G. E. Locus-specific knock-in of a degradable tag for target validation studies. Methods Mol. Biol. 1953, 105–119 (2019).
Lin, D. W. et al. Microhomology-based CRISPR tagging tools for protein tracking, purification, and depletion. J. Biol. Chem. 294, 10877–10885 (2019).
Wisniewski, J. R., Ostasiewicz, P. & Mann, M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J. Proteome Res. 10, 3040–3049 (2011).
Yeung, Y. G., Nieves, E., Angeletti, R. H. & Stanley, E. R. Removal of detergents from protein digests for mass spectrometry analysis. Anal. Biochem. 382, 135–137 (2008).
Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).
Gajduskova, P. et al. CDK11 is required for transcription of replication-dependent histone genes. Nat. Struct. Mol. Biol. 27, 500–510 (2020).
Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S. & Ralser, M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat. Methods 17, 41–44 (2020).
Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017).
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417 (2017).
Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118(2013).
West, C. et al. nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis. Wellcome Open Res. 8, 286 (2023).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A. & Manke, T. DeepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014).
Larsen, N. A. The SF3b complex is an integral component of the spliceosome and targeted by natural product-based inhibitors. Subcell. Biochem. 96, 409–432 (2021).
Acknowledgements
We wish to thank all members of the Blazek laboratory for discussions throughout the project and helpful comments on the manuscript. We also wish to thank Michal Rájecký and Veronika Gajdušková for help with the preparation of figures, Sebastian Fica and Wojciech Galej for discussions and initial help, and Dr. Wouters for the HCT116 Flp-in cell line. The work was supported by a grant from the Czech Science Foundation (23-04754X) to D.B, and funded by the European Union under Horizon Europe program HORIZON-WIDERA-2023-ACCESS-04, Grant Agreement No. 101159708–MILESTONE to K.T. CIISB, Instruct-CZ Center of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2023042 and European Regional Development Fund-Project „Innovation of Czech Infrastructure for Integrative Structural Biology“ (No. CZ.02.01.01/00/23_015/0008175), is gratefully acknowledged for the financial support of the measurements at the CEITEC Proteomics Core Facility. Computational resources were provided by the e-INFRA CZ project (ID:90254), supported by MEYS CR.
Author information
Authors and Affiliations
Contributions
P.G. performed most of the experiments and wrote the initial draft of the manuscript. I.R.dl.M. performed bioinformatics analyses of iCLIP- and RNA-seq, M.H. performed a chromatin MS experiment with SF3B1, A.M. and P.M. helped design and prepare the HCT116 dTAG SNIP1 cell line, N.D. prepared HCT116 F-SNIP1 cell lines, assisted with RT-PCR experiments and performed proliferation experiments, K.Z. performed AF3 modeling and evaluated the results, K.H., D.P. and Z.Z. performed and analyzed MS/MS experiments, S.B. performed protein isolation, J.N. and K.T. performed structural analyses, and C.C.F. performed bioinformatics analyses of dTAG SNIP1 and OTS964 RNA-seq data. D.B. supervised the research, wrote the initial draft of the manuscript and acquired funding. All authors discussed the design of experiments and commented on the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Communications thanks Ina Huppertz, Manoj Pillai and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Source data
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Gajdušková, P., Ruiz de Los Mozos, I., Hluchý, M. et al. Phosphorylation of SF3B1 by CDK11 orchestrates spliceosome activation via SNIP1-dependent RES complex recruitment. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71119-2
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41467-026-71119-2
