Current Genetics

, Volume 63, Issue 3, pp 375–380 | Cite as

The power of fission: yeast as a tool for understanding complex splicing

Review

Abstract

Pre-mRNA splicing is an essential component of eukaryotic gene expression. Many metazoans, including humans, regulate alternative splicing patterns to generate expansions of their proteome from a limited number of genes. Importantly, a considerable fraction of human disease causing mutations manifest themselves through altering the sequences that shape the splicing patterns of genes. Thus, understanding the mechanistic bases of this complex pathway will be an essential component of combating these diseases. Dating almost to the initial discovery of splicing, researchers have taken advantage of the genetic tractability of budding yeast to identify the components and decipher the mechanisms of splicing. However, budding yeast lacks the complex splicing machinery and alternative splicing patterns most relevant to humans. More recently, many researchers have turned their efforts to study the fission yeast, Schizosaccharomyces pombe, which has retained many features of complex splicing, including degenerate splice site sequences, the usage of exonic splicing enhancers, and SR proteins. Here, we review recent work using fission yeast genetics to examine pre-mRNA splicing, highlighting its promise for modeling the complex splicing seen in higher eukaryotes.

Keywords

Pre-mRNA splicing Schizosaccharomyces pombe SR proteins Alternative splicing Exon definition 

References

  1. Araya CL, Fowler DM (2011) Deep mutational scanning: assessing protein function on a massive scale. Trends Biotechnol 29:435–442CrossRefPubMedPubMedCentralGoogle Scholar
  2. Awan AR, Manfredo A, Pleiss JA (2013) Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans. Proc Natl Acad Sci 110:12762–12767. doi:10.1073/pnas.1218353110 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Barbosa-Morais NL, Irimia M, Pan Q et al (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338:1587–1593. doi:10.1126/science.1230612 CrossRefPubMedGoogle Scholar
  4. Berget SM (1995) Exon Recognition in Vertebrate Splicing. J Biol Chem 270:2411–2414. doi:10.1074/jbc.270.6.2411 CrossRefPubMedGoogle Scholar
  5. Bitton DA, Atkinson SR, Rallis C et al (2015) Widespread exon-skipping triggers degradation by nuclear RNA surveillance in fission yeast. Genome Res, pp 884–896. doi:10.1101/gr.185371.114
  6. Blencowe BJ, Baurén G, Eldridge AG et al (2000) The SRm160/300 splicing coactivator subunits. RNA N Y N 6:111–120. doi:10.1017/S1355838200991982 CrossRefGoogle Scholar
  7. Bradley RK, Merkin J, Lambert NJ, Burge CB (2012) Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol 10:e1001229. doi:10.1371/journal.pbio.1001229 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Clark TA, Sugnet CW, Ares M (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296:907–910. doi:10.1126/science.1069415 CrossRefPubMedGoogle Scholar
  9. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190. doi:10.1101/gr.849004 CrossRefPubMedPubMedCentralGoogle Scholar
  10. De Conti L, Baralle M, Buratti E (2013) Exon and intron definition in pre-mRNA splicing. Wiley Interdiscip Rev RNA 4:49–60. doi:10.1002/wrna.1140 CrossRefPubMedGoogle Scholar
  11. Eldridge AG, Li Y, Sharp PA, Blencowe BJ (1999) The SRm160/300 splicing coactivator is required for exon-enhancer function. Proc Natl Acad Sci 96:6125–6130. doi:10.1139/o99-903j CrossRefPubMedPubMedCentralGoogle Scholar
  12. Fowler DM, Fields S (2014) Deep mutational scanning: a new style of protein science. Nat Methods 11:801–807. doi:10.1038/nmeth.3027 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Gao K, Masuda A, Matsuura T, Ohno K (2008) Human branch point consensus sequence is yUnAy. Nucleic Acids Res 36:2257–2267. doi:10.1093/nar/gkn073 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Gao J, Kan F, Wagnon JL et al (2014) Rapid, efficient and precise allele replacement in the fission yeast Schizosaccharomyces pombe. Curr Genet 60:109–119. doi:10.1007/s00294-013-0406-x CrossRefPubMedGoogle Scholar
  15. Graveley BR (2000) Sorting out the complexity of SR protein functions. RNA N Y N 6:1197–1211. doi:10.1017/S1355838200000960 CrossRefGoogle Scholar
  16. Haraguchi N, Andoh T, Frendewey D, Tani T (2007) Mutations in the SF1-U2AF59-U2AF23 complex cause exon skipping in Schizosaccharomyces pombe. J Biol Chem 282:2221–2228. doi:10.1074/jbc.M609430200 CrossRefPubMedGoogle Scholar
  17. Hollander D, Naftelberg S, Lev-Maor G et al (2016) How are short exons flanked by long introns defined and committed to splicing? Trends Genet, pp 1–11. doi:10.1016/j.tig.2016.07.003 CrossRefGoogle Scholar
  18. Hossain MA, Johnson TL (2014) Using Yeast Genetics to Study Splicing Mechanisms. Methods Mol Biol 1126:285–298. doi:10.1007/978-1-62703-980-2_21 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Juneau K, Nislow C, Davis RW (2009) Alternative splicing of PTC7 in Saccharomyces cerevisiae determines protein localization. Genetics 183:185–194. doi:10.1534/genetics.109.105155 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Käufer NF, Potashkin J (2000) Analysis of the splicing machinery in fission yeast: a comparison with budding yeast and mammals. Nucleic Acids Res 28:3003–3010. doi:10.1093/nar/28.16.3003 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Kawashima T, Douglass S, Gabunilas J et al (2014) Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. PLoS Genet. doi:10.1371/journal.pgen.1004249 PubMedPubMedCentralGoogle Scholar
  22. Kent WJ, Sugnet CW, Furey TS et al (2002) The human genome browser at UCSC. Genome Res 12:996–1006. doi:10.1101/gr.229102 CrossRefPubMedPubMedCentralGoogle Scholar
  23. Kielkopf CL, Rodionova NA, Green MR, Burley SK (2001) A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer. Cell 106:595–605. doi:10.1016/S0092-8674(01)00480-9 CrossRefPubMedGoogle Scholar
  24. Kuhn AN, Käufer NF (2003) Pre-mRNA splicing in Schizosaccharomyces pombe: regulatory role of a kinase conserved from fission yeast to mammals. Curr Genet 42:241–251. doi:10.1007/s00294-002-0355-2 PubMedGoogle Scholar
  25. Larson A, Fair BJ, Pleiss JA (2016) Interconnections between RNA-processing pathways revealed by a sequencing-based genetic screen for pre-mRNA splicing mutants in fission yeast. G3 Bethesda Md 6:1513–23Google Scholar
  26. Lee Y, Rio DC (2015) Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem, pp 1–33. doi:10.1146/annurev-biochem-060614-034316
  27. Lipp JJ, Marvin MC, Shokat KM, Guthrie C (2015) SR protein kinases promote splicing of nonconsensus introns. Nat Struct Mol Biol 22:611–617. doi:10.1038/nsmb.3057 CrossRefPubMedGoogle Scholar
  28. Long JC, Caceres JF (2009) The SR protein family of splicing factors: master regulators of gene expression. Biochem J 417:15–27. doi:10.1042/BJ20081501 CrossRefPubMedGoogle Scholar
  29. Lustig AJ, Lin RJ, Abelson J (1986) The yeast RNA gene products are essential for mRNA splicing in vitro. Cell 47:953–963CrossRefPubMedGoogle Scholar
  30. Marshall AN, Montealegre MC, Jiménez-López C et al (2013) Alternative splicing and subfunctionalization generates functional diversity in fungal proteomes. PLoS Genet. doi:10.1371/journal.pgen.1003376 Google Scholar
  31. Matlin AJ, Clark F, Smith CWJ (2005) Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6:386–398. doi:10.1038/nrm1645 CrossRefPubMedGoogle Scholar
  32. Mazroui R, Puoti A, Krämer A (1999) Splicing factor SF1 from Drosophila and Caenorhabditis: presence of an N-terminal RS domain and requirement for viability. RNA N Y N 5:1615–1631. doi:10.1017/S1355838299991872 CrossRefGoogle Scholar
  33. Meyer M, Vilardell J (2009) The quest for a message: budding yeast, a model organism to study the control of pre-mRNA splicing. Brief Funct Genomic Proteomic 8:60–67. doi:10.1093/bfgp/elp002 CrossRefPubMedGoogle Scholar
  34. Nguyen THD, Galej WP, Bai X et al (2015) The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Nature 523:47–52. doi:10.1038/nature14548 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Nguyen THD, Galej WP, Fica SM et al (2016) CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast. Curr Opin Struct Biol 36:48–57CrossRefPubMedPubMedCentralGoogle Scholar
  36. Noble SM, Guthrie C (1996) Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations. Genetics 143:67–80PubMedPubMedCentralGoogle Scholar
  37. 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. doi:10.1016/j.molcel.2013.03.001 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Patrick KL, Ryan CJ, Xu J et al (2015) Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast. PLoS Genet 11:e1005074. doi:10.1371/journal.pgen.1005074 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Ram O, Ast G (2007) SR proteins: a foot on the exon before the transition from intron to exon definition. Trends Genet 23:5–7. doi:10.1016/j.tig.2006.10.002 CrossRefPubMedGoogle Scholar
  40. Robberson BL, Cote GJ, Berget SM (1990) Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol Cell Biol 10:84–94. doi:10.1128/MCB.10.1.84.Updated CrossRefPubMedPubMedCentralGoogle Scholar
  41. Romfo CM, Alvarez CJ, van Heeckeren WJ et al (2000) Evidence for splice site pairing via intron definition in Schizosaccharomyces pombe. Mol Cell Biol 20:7955–7970CrossRefPubMedPubMedCentralGoogle Scholar
  42. Sasaki-Haraguchi N, Ikuyama T, Yoshii S et al (2015) Cwf16p associating with the nineteen complex ensures ordered exon joining in constitutive Pre-mRNA splicing in fission yeast. PLoS One 10:1–16. doi:10.1371/journal.pone.0136336 CrossRefGoogle Scholar
  43. Scheckel C, Darnell RB (2015) Microexons—tiny but mighty. EMBO J 34:273–274. doi:10.15252/embj.201490651 CrossRefPubMedGoogle Scholar
  44. Shao C, Yang B, Wu T et al (2014) Mechanisms for U2AF to define 3′ splice sites and regulate alternative splicing in the human genome. Nat Struct Mol Biol 21:997–1005. doi:10.1038/nsmb.2906 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Stepankiw N, Raghavan M, Fogarty EA et al (2015) Widespread alternative and aberrant splicing revealed by lariat sequencing. Nucleic Acids Res 43:8488–8501CrossRefPubMedPubMedCentralGoogle Scholar
  46. Szymczyna BR, Bowman J, McCracken S et al (2003) Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing. Genes Dev 17:461–475. doi:10.1101/gad.1060403 CrossRefPubMedPubMedCentralGoogle Scholar
  47. Vijayraghavan U, Company M, Abelson J (1989) Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev 3:1206–1216. doi:10.1101/gad.3.8.1206 CrossRefPubMedGoogle Scholar
  48. Vo TV, Das J, Meyer MJ et al (2016) A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human. Cell 164:310–323. doi:10.1016/j.cell.2015.11.037 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Wahl MC, Will CL, Lührmann R (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136:701–718. doi:10.1016/j.cell.2009.02.009 CrossRefPubMedGoogle Scholar
  50. Webb CJ, Wise JA (2004) The splicing factor U2AF small subunit is functionally conserved between fission yeast and humans. Mol Cell Biol 24:4229–4240. doi:10.1128/MCB.24.10.4229 CrossRefPubMedPubMedCentralGoogle Scholar
  51. Webb CJ, Romfo CM, van Heeckeren WJ, Wise JA (2005) Exonic splicing enhancers in fission yeast: functional conservation demonstrates an early evolutionary origin. Genes Dev 19:242–254. doi:10.1101/gad.1265905 CrossRefPubMedPubMedCentralGoogle Scholar
  52. Wilhelm BT, Marguerat S, Watt S et al (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453:1239–1243. doi:10.1038/nature07002 CrossRefPubMedGoogle Scholar
  53. Will CL, Lührmann R (2011) Spliceosome structure and function. Cold Spring Harb Perspect Biol 3:1–2. doi:10.1101/cshperspect.a003707 CrossRefGoogle Scholar
  54. Yan C, Hang J, Wan R et al (2015) Structure of a yeast spliceosome at 3.6-angstrom resolution. Science 349:1182–1191CrossRefPubMedGoogle Scholar
  55. Zuo P, Maniatis T (1996) The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. Genes Dev 10:1356–1368. doi:10.1101/gad.10.11.1356 CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of Molecular Biology and GeneticsCornell UniversityIthacaUSA

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