SRSF3 and SRSF7 Modulate 3'UTR Length Through Suppression or Activation of Proximal Polyadenylation Sites and Regulation of CFIm Levels

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2021 Mar 12

PMID 33706811

Citations 23

Authors

Oliver Daniel Schwich

Nicole Blumel

Mario Keller

Marius Wegener

Samarth Thonta Setty

Melinda Elaine Brunstein

Ina Poser

Igor Ruiz de Los Mozos

Beatrix Suess

Christian Munch

Francois McNicoll

Kathi Zarnack

Michaela Muller-McNicoll

Affiliations

Soon will be listed here.

Abstract

Background: Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3' untranslated regions (3'UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown.

Results: Here we combine iCLIP and 3'-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3'UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3'UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3'UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3'UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3'UTRs.

Conclusions: We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation.

Citing Articles

At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.

Koster T, Venhuizen P, Lewinski M, Petrillo E, Marquez Y, Fuchs A bioRxiv. 2024; .

PMID: 39677721 PMC: 11643119. DOI: 10.1101/2024.12.04.626797.

Coupling of alternative splicing and alternative polyadenylation.

Zhang X, Liu F, Zhou Y Acta Biochim Biophys Sin (Shanghai). 2024; 57(1):22-32.

PMID: 39632657 PMC: 11802343. DOI: 10.3724/abbs.2024211.

Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination.

Grzechnik P, Mischo H J Mol Biol. 2024; 437(1):168802.

PMID: 39321865 PMC: 11870849. DOI: 10.1016/j.jmb.2024.168802.

Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression.

Van Goubergen J, Perina M, Handle F, Morales E, Kremer A, Schmidt O Mol Oncol. 2024; 19(2):496-518.

PMID: 39258426 PMC: 11792998. DOI: 10.1002/1878-0261.13728.

Systematic identification of post-transcriptional regulatory modules.

Khoroshkin M, Buyan A, Dodel M, Navickas A, Yu J, Trejo F Nat Commun. 2024; 15(1):7872.

PMID: 39251607 PMC: 11385195. DOI: 10.1038/s41467-024-52215-7.

References

Takagaki Y, Ryner L, Manley J . Four factors are required for 3'-end cleavage of pre-mRNAs. Genes Dev. 1989; 3(11):1711-24. DOI: 10.1101/gad.3.11.1711. View

Chan S, Huppertz I, Yao C, Weng L, Moresco J, Yates 3rd J . CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing. Genes Dev. 2014; 28(21):2370-80. PMC: 4215182. DOI: 10.1101/gad.250993.114. View

Neve J, Patel R, Wang Z, Louey A, Furger A . Cleavage and polyadenylation: Ending the message expands gene regulation. RNA Biol. 2017; 14(7):865-890. PMC: 5546720. DOI: 10.1080/15476286.2017.1306171. View

Kaida D, Berg M, Younis I, Kasim M, Singh L, Wan L . U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature. 2010; 468(7324):664-8. PMC: 2996489. DOI: 10.1038/nature09479. View

Kumar D, Das M, Sauceda C, Ellies L, Kuo K, Parwal P . Degradation of splicing factor SRSF3 contributes to progressive liver disease. J Clin Invest. 2019; 129(10):4477-4491. PMC: 6763247. DOI: 10.1172/JCI127374. View

Lou H, Neugebauer K, Gagel R, Berget S . Regulation of alternative polyadenylation by U1 snRNPs and SRp20. Mol Cell Biol. 1998; 18(9):4977-85. PMC: 109082. DOI: 10.1128/MCB.18.9.4977. View

Masamha C, Xia Z, Yang J, Albrecht T, Li M, Shyu A . CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature. 2014; 510(7505):412-6. PMC: 4128630. DOI: 10.1038/nature13261. View

Muller S, Rycak L, Afonso-Grunz F, Winter P, Zawada A, Damrath E . APADB: a database for alternative polyadenylation and microRNA regulation events. Database (Oxford). 2014; 2014. PMC: 4105710. DOI: 10.1093/database/bau076. View

Nakayama Y, Wada A, Inoue R, Terasawa K, Kimura I, Nakamura N . A rapid and efficient method for neuronal induction of the P19 embryonic carcinoma cell line. J Neurosci Methods. 2014; 227:100-6. DOI: 10.1016/j.jneumeth.2014.02.011. View

10.

Chatrikhi R, Mallory M, Gazzara M, Agosto L, Zhu W, Litterman A . RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery. Cell Rep. 2019; 28(11):2795-2806.e3. PMC: 6752737. DOI: 10.1016/j.celrep.2019.08.022. View

11.

Cavaloc Y, Bourgeois C, Kister L, Stevenin J . The splicing factors 9G8 and SRp20 transactivate splicing through different and specific enhancers. RNA. 1999; 5(3):468-83. PMC: 1369774. DOI: 10.1017/s1355838299981967. View

12.

Valente T, Zogg J, Christensen S, Richardson J, Kovacs A, Operskalski E . Using social networks to recruit an HIV vaccine preparedness cohort. J Acquir Immune Defic Syndr. 2009; 52(4):514-23. PMC: 2783777. DOI: 10.1097/QAI.0b013e3181acff91. View

13.

Ruegsegger U, Beyer K, Keller W . Purification and characterization of human cleavage factor Im involved in the 3' end processing of messenger RNA precursors. J Biol Chem. 1996; 271(11):6107-13. DOI: 10.1074/jbc.271.11.6107. View

14.

Gruber A, Zavolan M . Alternative cleavage and polyadenylation in health and disease. Nat Rev Genet. 2019; 20(10):599-614. DOI: 10.1038/s41576-019-0145-z. View

15.

Xia Z, Donehower L, Cooper T, Neilson J, Wheeler D, Wagner E . Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun. 2014; 5:5274. PMC: 4467577. DOI: 10.1038/ncomms6274. View

16.

Surendranath V, Theis M, Habermann B, Buchholz F . Designing efficient and specific endoribonuclease-prepared siRNAs. Methods Mol Biol. 2012; 942:193-204. DOI: 10.1007/978-1-62703-119-6_11. View

17.

Mandel C, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley J . Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Nature. 2006; 444(7121):953-6. PMC: 3866582. DOI: 10.1038/nature05363. View

18.

Anko M, Muller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I . The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol. 2012; 13(3):R17. PMC: 3439968. DOI: 10.1186/gb-2012-13-3-r17. View

19.

Xiao S, Manley J . Phosphorylation of the ASF/SF2 RS domain affects both protein-protein and protein-RNA interactions and is necessary for splicing. Genes Dev. 1997; 11(3):334-44. DOI: 10.1101/gad.11.3.334. View

20.

Martin G, Gruber A, Keller W, Zavolan M . Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. Cell Rep. 2012; 1(6):753-63. DOI: 10.1016/j.celrep.2012.05.003. View