Oliver Daniel Schwich1,2, Nicole Blümel1, Mario Keller2,3, Marius Wegener1,2, Samarth Thonta Setty2, Melinda Elaine Brunstein4, Ina Poser5, Igor Ruiz De Los Mozos6, Beatrix Suess7, Christian Münch4, François McNicoll1, Kathi Zarnack8,9, Michaela Müller-McNicoll10. 1. Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany. 2. Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. 3. Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany. 4. Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany. 5. Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany. 6. The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. 7. Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany. 8. Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. kathi.zarnack@bmls.de. 9. Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany. kathi.zarnack@bmls.de. 10. Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany. mueller-mcnicoll@bio.uni-frankfurt.de.
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.
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.
Authors: Serena L Chan; Ina Huppertz; Chengguo Yao; Lingjie Weng; James J Moresco; John R Yates; Jernej Ule; James L Manley; Yongsheng Shi Journal: Genes Dev Date: 2014-10-09 Impact factor: 11.361
Authors: Rakesh Chatrikhi; Michael J Mallory; Matthew R Gazzara; Laura M Agosto; Wandi S Zhu; Adam J Litterman; K Mark Ansel; Kristen W Lynch Journal: Cell Rep Date: 2019-09-10 Impact factor: 9.423
Authors: Souvik Ghosh; Meric Ataman; Maciej Bak; Anastasiya Börsch; Alexander Schmidt; Katarzyna Buczak; Georges Martin; Beatrice Dimitriades; Christina J Herrmann; Alexander Kanitz; Mihaela Zavolan Journal: Nucleic Acids Res Date: 2022-04-08 Impact factor: 16.971
Authors: Andrew M Jobbins; Nejc Haberman; Natalia Artigas; Christopher Amourda; Helen A B Paterson; Sijia Yu; Samuel J I Blackford; Alex Montoya; Marian Dore; Yi-Fang Wang; Alessandro Sardini; Inês Cebola; Johannes Zuber; Sheikh Tamir Rashid; Boris Lenhard; Santiago Vernia Journal: Nucleic Acids Res Date: 2022-04-08 Impact factor: 16.971
Authors: Marie E Gaine; Ethan Bahl; Snehajyoti Chatterjee; Jacob J Michaelson; Ted Abel; Lisa C Lyons Journal: Mol Brain Date: 2021-08-12 Impact factor: 4.399
Authors: Hsin-Wei Tseng; Anthony Mota-Sydor; Rania Leventis; Predrag Jovanovic; Ivan Topisirovic; Thomas F Duchaine Journal: Nucleic Acids Res Date: 2022-08-22 Impact factor: 19.160