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Widespread Use of Non-productive Alternative Splice Sites in
Accurate gene expression requires the transfer of gene information from DNA to RNA. When DNA is transcribed into RNA, part of the RNA needs to be removed (spliced) to generate a proper copy of the genetic information. This process needs to be very accurate to preserve the genetic information that will be transferred into proteins. Our study shows that in baker's yeast, the splicing process does not always produce the correctly spliced products, as RNA splicing events frequently utilize incorrect splice sites. However, these deficient RNA molecules are eliminated from cells by a quality control mechanism to preserve the integrity of the genetic information. However, incorrect splicing is not useless, as it can be used to regulate the quantity of RNA that is generated.
Vyšlo v časopise: Widespread Use of Non-productive Alternative Splice Sites in. PLoS Genet 10(4): e32767. doi:10.1371/journal.pgen.1004249
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004249Souhrn
Accurate gene expression requires the transfer of gene information from DNA to RNA. When DNA is transcribed into RNA, part of the RNA needs to be removed (spliced) to generate a proper copy of the genetic information. This process needs to be very accurate to preserve the genetic information that will be transferred into proteins. Our study shows that in baker's yeast, the splicing process does not always produce the correctly spliced products, as RNA splicing events frequently utilize incorrect splice sites. However, these deficient RNA molecules are eliminated from cells by a quality control mechanism to preserve the integrity of the genetic information. However, incorrect splicing is not useless, as it can be used to regulate the quantity of RNA that is generated.
Zdroje
1. IskenO, MaquatLE (2007) Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev 21 : 1833–1856.
2. KervestinS, JacobsonA (2012) NMD: a multifaceted response to premature translational termination. Nat Rev Mol Cell Biol 13 : 700–712.
3. GreenRE, LewisBP, HillmanRT, BlanchetteM, LareauLF, et al. (2003) Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 19 (Suppl 1) i118–121.
4. LareauLF, InadaM, GreenRE, WengrodJC, BrennerSE (2007) Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446 : 926–929.
5. NiJZ, GrateL, DonohueJP, PrestonC, NobidaN, et al. (2007) Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 21 : 708–718.
6. MendellJT, SharifiNA, MeyersJL, Martinez-MurilloF, DietzHC (2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet 36 : 1073–1078.
7. ChanWK, HuangL, GudikoteJP, ChangYF, ImamJS, et al. (2007) An alternative branch of the nonsense-mediated decay pathway. EMBO J 26 : 1820–1830.
8. WeischenfeldtJ, DamgaardI, BryderD, Theilgaard-MonchK, ThorenLA, et al. (2008) NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements. Genes Dev 22 : 1381–1396.
9. HeF, PeltzSW, DonahueJL, RosbashM, JacobsonA (1993) Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1 - mutant. Proc Natl Acad Sci U S A 90 : 7034–7038.
10. MitrovichQM, AndersonP (2000) Unproductively spliced ribosomal protein mRNAs are natural targets of mRNA surveillance in C. elegans. Genes Dev 14 : 2173–2184.
11. JaillonO, BouhoucheK, GoutJF, AuryJM, NoelB, et al. (2008) Translational control of intron splicing in eukaryotes. Nature 451 : 359–362.
12. SayaniS, JanisM, LeeCY, ToescaI, ChanfreauGF (2008) Widespread impact of nonsense-mediated mRNA decay on the yeast intronome. Mol Cell 31 : 360–370.
13. SayaniS, ChanfreauGF (2012) Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae. RNA 18 : 1563–1572.
14. VijayraghavanU, CompanyM, AbelsonJ (1989) Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev 3 : 1206–1216.
15. WahlMC, WillCL, LuhrmannR (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136 : 701–718.
16. GrundSE, FischerT, CabalGG, AntunezO, Perez-OrtinJE, et al. (2008) The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression. J Cell Biol 182 : 897–910.
17. MishraSK, AmmonT, PopowiczGM, KrajewskiM, NagelRJ, et al. (2011) Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature 474 : 173–178.
18. MeyerM, PlassM, Perez-ValleJ, EyrasE, VilardellJ (2011) Deciphering 3′ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing. Mol Cell 43 : 1033–1039.
19. PlassM, Codony-ServatC, FerreiraPG, VilardellJ, EyrasE (2012) RNA secondary structure mediates alternative 3′ss selection in Saccharomyces cerevisiae. RNA 18 : 1103–1115.
20. MarshallAN, MontealegreMC, Jimenez-LopezC, LorenzMC, van HoofA (2013) Alternative splicing and subfunctionalization generates functional diversity in fungal proteomes. PLoS Genet 9: e1003376.
21. KawashimaT, PellegriniM, ChanfreauGF (2009) Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations. RNA 15 : 2236–2247.
22. KentWJ (2002) BLAT–the BLAST-like alignment tool. Genome Res 12 : 656–664.
23. LiaoXC, TangJ, RosbashM (1993) An enhancer screen identifies a gene that encodes the yeast U1 snRNP A protein: implications for snRNP protein function in pre-mRNA splicing. Genes Dev 7 : 419–428.
24. NeubauerG, GottschalkA, FabrizioP, SeraphinB, LuhrmannR, et al. (1997) Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc Natl Acad Sci U S A 94 : 385–390.
25. PuigO, GottschalkA, FabrizioP, SeraphinB (1999) Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection. Genes Dev 13 : 569–580.
26. GottschalkA, TangJ, PuigO, SalgadoJ, NeubauerG, et al. (1998) A comprehensive biochemical and genetic analysis of the yeast U1 snRNP reveals five novel proteins. RNA 4 : 374–393.
27. UmenJG, GuthrieC (1995) Prp16p, Slu7p, and Prp8p interact with the 3′ splice site in two distinct stages during the second catalytic step of pre-mRNA splicing. RNA 1 : 584–597.
28. AronovaA, BacíkováD, CrottiLB, HorowitzDS, SchwerB (2007) Functional interactions between Prp8, Prp18, Slu7, and U5 snRNA during the second step of pre-mRNA splicing. RNA 13 : 1437–1444.
29. VillaT, GuthrieC (2005) The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing. Genes Dev 19 : 1894–1904.
30. SahaD, BanerjeeS, BashirS, VijayraghavanU (2012) Context dependent splicing functions of Bud31/Ycr063w define its role in budding and cell cycle progression. Biochem Biophys Res Commun 424 : 579–585.
31. Rodriguez-NavarroS, IgualJC, Perez-OrtinJE (2002) SRC1: an intron-containing yeast gene involved in sister chromatid segregation. Yeast 19 : 43–54.
32. ChanfreauGF (2010) A dual role for RNA splicing signals. EMBO Rep 11 : 720–721.
33. CrottiLB, HorowitzDS (2009) Exon sequences at the splice junctions affect splicing fidelity and alternative splicing. Proc Natl Acad Sci U S A 106 : 18954–18959.
34. ZhouY, ChenC, JohanssonMJ (2013) The pre-mRNA retention and splicing complex controls tRNA maturation by promoting TAN1 expression. Nucleic Acids Res 41 : 5669–5678.
35. YanBC, WestfallBA, OrleanP (2001) Ynl038wp (Gpi15p) is the Saccharomyces cerevisiae homologue of human Pig-Hp and participates in the first step in glycosylphosphatidylinositol assembly. Yeast 18 : 1383–1389.
36. MuhlradD, ParkerR (1999) Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance. RNA 5 : 1299–1307.
37. AmraniN, GanesanR, KervestinS, MangusDA, GhoshS, et al. (2004) A faux 3′-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature 432 : 112–118.
38. UemuraH, JigamiY (1995) Mutations in GCR1, a transcriptional activator of Saccharomyces cerevisiae glycolytic genes, function as suppressors of gcr2 mutations. Genetics 139 : 511–521.
39. HollandMJ, YokoiT, HollandJP, MyamboK, InnisMA (1987) The GCR1 gene encodes a positive transcriptional regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families in Saccharomyces cerevisiae. Mol Cell Biol 7 : 813–820.
40. CliftonD, FraenkelDG (1981) The gcr (glycolysis regulation) mutation of Saccharomyces cerevisiae. J Biol Chem 256 : 13074–13078.
41. MayasRM, MaitaH, StaleyJP (2006) Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat Struct Mol Biol 13 : 482–490.
42. JamesSA, TurnerW, SchwerB (2002) How Slu7 and Prp18 cooperate in the second step of yeast pre-mRNA splicing. RNA 8 : 1068–1077.
43. BergkesselM, WhitworthGB, GuthrieC (2011) Diverse environmental stresses elicit distinct responses at the level of pre-mRNA processing in yeast. RNA 17 : 1461–1478.
44. PleissJA, WhitworthGB, BergkesselM, GuthrieC (2007) Rapid, transcript-specific changes in splicing in response to environmental stress. Mol Cell 27 : 928–937.
45. LiB, NierrasCR, WarnerJR (1999) Transcriptional elements involved in the repression of ribosomal protein synthesis. Mol Cell Biol 19 : 5393–5404.
46. GaschAP, SpellmanPT, KaoCM, Carmel-HarelO, EisenMB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11 : 4241–4257.
47. GarreE, Romero-SantacreuL, Barneo-MunozM, MiguelA, Perez-OrtinJE, et al. (2013) Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress. PLoS One 8: e61240.
48. YostHJ, LindquistS (1991) Heat shock proteins affect RNA processing during the heat shock response of Saccharomyces cerevisiae. Mol Cell Biol 11 : 1062–1068.
49. VogelJL, ParsellDA, LindquistS (1995) Heat-shock proteins Hsp104 and Hsp70 reactivate mRNA splicing after heat inactivation. Curr Biol 5 : 306–317.
50. AwanAR, ManfredoA, PleissJA (2013) Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans. Proc Natl Acad Sci U S A 110 : 12762–12767.
51. HulsenT, de VliegJ, AlkemaW (2008) BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics 9 : 488.
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Genetika Reprodukčná medicína
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