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SRSF2 directly inhibits intron splicing to suppresses cassette exon inclusion

  • Moon, Heegyum (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Cho, Sunghee (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Loh, Tiing Jen (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Jang, Ha Na (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Liu, Yongchao (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Choi, Namjeong (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Oh, Jagyeong (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Ha, Jiyeon (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Zhou, Jianhua (JiangSu Key Laboratory of Neuroregeneration, Nantong University) ;
  • Cho, Sungchan (Bio-Therapeutics Research Institute, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Dong-Eun (Department of Bioscience and Biotechnology, Konkuk University) ;
  • Ye, Michael B. (Division of Liberal Arts and Sciences, Gwangju Institute of Science and Technology) ;
  • Zheng, Xuexiu (School of Life Sciences, Gwangju Institute of Science and Technology) ;
  • Shen, Haihong (School of Life Sciences, Gwangju Institute of Science and Technology)
  • Received : 2017.06.16
  • Accepted : 2017.07.17
  • Published : 2017.08.31

Abstract

SRSF2, a Serine-Arginine rich (SR) protein, is a splicing activator that mediates exon inclusion and exclusion events equally well. Here we show SRSF2 directly suppresses intron splicing to suppress cassette exon inclusion in SMN pre-mRNA. Through a serial mutagenesis, we demonstrate that a 10 nt RNA sequence surrounding the branch-point (BP), is important for SRSF2-mediated inhibition of cassette exon inclusion through directly interacting with SRSF2. We conclude that SRSF2 inhibits intron splicing to promote exon exclusion.

Keywords

References

  1. Wahl MC, Will CL and Luhrmann R (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701-718 https://doi.org/10.1016/j.cell.2009.02.009
  2. Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72, 291-336 https://doi.org/10.1146/annurev.biochem.72.121801.161720
  3. Fu XD and Ares M Jr (2014) Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15, 689-701 https://doi.org/10.1038/nrg3778
  4. Ghigna C, Valacca C and Biamonti G (2008) Alternative splicing and tumor progression. Curr Genomics 9, 556-570 https://doi.org/10.2174/138920208786847971
  5. Park SA, Ahn SI and Gallo JM (2016) Tau mis-splicing in the pathogenesis of neurodegenerative disorders. BMB Rep 49, 405-413 https://doi.org/10.5483/BMBRep.2016.49.8.084
  6. Singh RK and Cooper TA (2012) Pre-mRNA splicing in disease and therapeutics. Trends Mol Med 18, 472-482 https://doi.org/10.1016/j.molmed.2012.06.006
  7. Cho S, Moon H, Loh TJ et al (2015) Splicing inhibition of U2AF65 leads to alternative exon skipping. Proc Natl Acad Sci U S A 112, 9926-9931 https://doi.org/10.1073/pnas.1500639112
  8. Kashima T, Rao N, David CJ and Manley JL (2007) hnRNP A1 functions with specificity in repression of SMN2 exon 7 splicing. Hum Mol Genet 16, 3149-3159 https://doi.org/10.1093/hmg/ddm276
  9. Blencowe BJ, Bowman JA, McCracken S and Rosonina E (1999) SR-related proteins and the processing of messenger RNA precursors. Biochem Cell Biol 77, 277-291 https://doi.org/10.1139/o99-048
  10. Fu XD (1995) The superfamily of arginine/serine-rich splicing factors. RNA 1, 663-680
  11. Loh TJ, Moon H, Jang HN et al (2016) SR proteins regulate V6 exon splicing of CD44 pre-mRNA. BMB Rep 49, 612-616 https://doi.org/10.5483/BMBRep.2016.49.11.118
  12. Shen H and Green MR (2004) A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly. Mol Cell 16, 363-373 https://doi.org/10.1016/j.molcel.2004.10.021
  13. Shen H, Kan JL and Green MR (2004) Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. Mol Cell 13, 367-376 https://doi.org/10.1016/S1097-2765(04)00025-5
  14. Hertel KJ and Graveley BR (2005) RS domains contact the pre-mRNA throughout spliceosome assembly. Trends Biochem Sci 30, 115-118 https://doi.org/10.1016/j.tibs.2005.01.002
  15. Daubner GM, Clery A, Jayne S, Stevenin J and Allain FH (2012) A syn-anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well. EMBO J 31, 162-174 https://doi.org/10.1038/emboj.2011.367
  16. Tacke R and Manley JL (1995) The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J 14, 3540-3551
  17. Shin C and Manley JL (2002) The SR protein SRp38 represses splicing in M phase cells. Cell 111, 407-417 https://doi.org/10.1016/S0092-8674(02)01038-3
  18. Simard MJ and Chabot B (2002) SRp30c is a repressor of 3' splice site utilization. Mol Cell Biol 22, 4001-4010 https://doi.org/10.1128/MCB.22.12.4001-4010.2002
  19. Singh NN, Androphy EJ and Singh RN (2004) In vivo selection reveals combinatorial controls that define a critical exon in the spinal muscular atrophy genes. RNA 10, 1291-1305 https://doi.org/10.1261/rna.7580704
  20. Buratti E, Stuani C, De Prato G and Baralle FE (2007) SR protein-mediated inhibition of CFTR exon 9 inclusion: molecular characterization of the intronic splicing silencer. Nucleic Acids Res 35, 4359-4368 https://doi.org/10.1093/nar/gkm444
  21. Pandit S, Zhou Y, Shiue L et al (2013) Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell 50, 223-235 https://doi.org/10.1016/j.molcel.2013.03.001
  22. Wee CD, Havens MA, Jodelka FM and Hastings ML (2014) Targeting SR proteins improves SMN expression in spinal muscular atrophy cells. PLoS One 9, e115205 https://doi.org/10.1371/journal.pone.0115205
  23. Cho S, Moon H, Loh TJ et al (2014) hnRNP M facilitates exon 7 inclusion of SMN2 pre-mRNA in spinal muscular atrophy by targeting an enhancer on exon 7. Biochim Biophys Acta 1839, 306-315 https://doi.org/10.1016/j.bbagrm.2014.02.006
  24. Fu XD and Maniatis T (1992) The 35-kDa mammalian splicing factor SC35 mediates specific interactions between U1 and U2 small nuclear ribonucleoprotein particles at the 3' splice site. Proc Natl Acad Sci U S A 89, 1725-1729 https://doi.org/10.1073/pnas.89.5.1725
  25. Wang J and Manley JL (1995) Overexpression of the SR proteins ASF/SF2 and SC35 influences alternative splicing in vivo in diverse ways. RNA 1, 335-346
  26. Shen H, Zheng X, Luecke S and Green MR (2010) The U2AF35-related protein Urp contacts the 3' splice site to promote U12-type intron splicing and the second step of U2-type intron splicing. Genes Dev 24, 2389-2394 https://doi.org/10.1101/gad.1974810
  27. Cartegni L, Wang J, Zhu Z, Zhang MQ and Krainer AR (2003) ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res 31, 3568-3571 https://doi.org/10.1093/nar/gkg616
  28. Fu XD and Maniatis T (1990) Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343, 437-441 https://doi.org/10.1038/343437a0
  29. Valcarcel J, Gaur RK, Singh R and Green MR (1996) Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA [corrected]. Science 273, 1706-1709 https://doi.org/10.1126/science.273.5282.1706
  30. Han J, Ding JH, Byeon CW et al (2011) SR proteins induce alternative exon skipping through their activities on the flanking constitutive exons. Mol Cell Biol 31, 793-802 https://doi.org/10.1128/MCB.01117-10
  31. Ghigna C, Giordano S, Shen H et al (2005) Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Mol Cell 20, 881-890 https://doi.org/10.1016/j.molcel.2005.10.026
  32. Erkelenz S, Mueller WF, Evans MS et al (2013) Positiondependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms. RNA 19, 96-102 https://doi.org/10.1261/rna.037044.112
  33. Zheng X, Cho S, Moon H, Loh TJ, Jang HN and Shen H (2016) Detecting RNA-Protein Interaction Using End-Labeled Biotinylated RNA Oligonucleotides and Immunoblotting. Methods Mol Biol 1421, 35-44
  34. Moon H, Cho S, Loh TJ et al (2014) SRSF2 promotes splicing and transcription of exon 11 included isoform in Ron proto-oncogene. Biochim Biophys Acta 1839, 1132-1140 https://doi.org/10.1016/j.bbagrm.2014.09.003