Minor Intron Splicing: Comparison
Please note this is a comparison between Version 2 by Conner Chen and Version 1 by Ettaib El Marabti.

Pre-mRNA splicing is an essential step in gene expression and is catalyzed by two machineries in eukaryotes: the major (U2 type) and minor (U12 type) spliceosomes. While the majority of introns in humans are U2 type, less than 0.4% are U12 type, also known as minor introns (mi-INTs), and require a specialized spliceosome composed of U11, U12, U4atac, U5, and U6atac snRNPs. The high evolutionary conservation and apparent splicing inefficiency of U12 introns have set them apart from their major counterparts and led to speculations on the purpose for their existence.

  • minor introns
  • U2 introns
  • U12 introns
  • minor spliceosome
  • RNA splicing
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References

  1. Kruger, K.; Grabowski, P.J.; Zaug, A.J.; Sands, J.; Gottschling, D.E.; Cech, T.R. Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena. Cell 1982, 31, 147–157.
  2. Guerrier-Takada, C.; Gardiner, K.; Marsh, T.; Pace, N.; Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 1983, 35, 849–857.
  3. Wolff, J.A.; Malone, R.W.; Williams, P.; Chong, W.; Acsadi, G.; Jani, A.; Felgner, P.L. Direct gene transfer into mouse muscle in vivo. Science 1990, 247, 1465–1468.
  4. Martinon, F.; Krishnan, S.; Lenzen, G.; Magné, R.; Gomard, E.; Guillet, J.-G.; Lévy, J.-P.; Meulien, P. Induction of virus-specific cytotoxic T lymphocytesin vivo by liposome-entrapped mRNA. Eur. J. Immunol. 1993, 23, 1719–1722.
  5. Polack, F.P.; Thomas, S.J.; Kitchin, N.; Absalon, J.; Gurtman, A.; Lockhart, S.; Perez, J.L.; Marc, G.P.; Moreira, E.D.; Zerbini, C.; et al. Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N. Engl. J. Med. 2020, 383, 2603–2615.
  6. Jackson, L.A.; Anderson, E.J.; Rouphael, N.G.; Roberts, P.C.; Makhene, M.; Coler, R.N.; McCullough, M.P.; Chappell, J.D.; Denison, M.R.; Stevens, L.J.; et al. An mRNA Vaccine against SARS-CoV-2—Preliminary Report. N. Engl. J. Med. 2020, 383, 1920–1931.
  7. Abelson, J. RNA Processing and the Intervening Sequence Problem. Annu. Rev. Biochem. 1979, 48, 1035–1069.
  8. Green, M.R. PRE-mRNA Splicing. Ann. Rev. Genet. 1986, 20, 671–708.
  9. Padgett, R.A.; Grabowski, P.J.; Konarska, M.M.; Seiler, S.; Sharp, P.A. Splicing of Messenger RNA Precursors. Annu. Rev. Biochem. 1986, 55, 1119–1150.
  10. El Marabti, E.; Younis, I. The Cancer Spliceome: Reprograming of Alternative Splicing in Cancer. Front. Mol. Biosci. 2018, 5, 80.
  11. Will, C.L.; Lührmann, R. Spliceosome structure and function. Cold Spring Harb. Perspect. Biol. 2011, 3, 1–2.
  12. Hall, S.L.; Padgett, R. Conserved Sequences in a Class of Rare Eukaryotic Nuclear Introns with Non-consensus Splice Sites. J. Mol. Biol. 1994, 239, 357–365.
  13. Tarn, W.-Y.; Steitz, J.A. A Novel Spliceosome Containing U11, U12, and U5 snRNPs Excises a Minor Class (AT–AC) Intron In Vitro. Cell 1996, 84, 801–811.
  14. Patel, A.A.; Steitz, J.A. Splicing double: Insights from the second spliceosome. Nat. Rev. Mol. Cell Biol. 2003, 4, 960–970.
  15. Hall, S.L.; Padgett, R.A. Requirement of U12 snRNA for in Vivo Splicing of a Minor Class of Eukaryotic Nuclear Pre-mRNA Introns. Science 1996, 271, 1716–1718.
  16. Jackson, L.J. A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res. 1991, 19, 3795–3798.
  17. Dietrich, R.C.; Incorvaia, R.A.; Padgett, R. Terminal Intron Dinucleotide Sequences Do Not Distinguish between U2- and U12-Dependent Introns. Mol. Cell 1997, 1, 151–160.
  18. Sharp, P.A.; Burge, C.B. Classification of Introns: U2-Type or U12-Type. Cell 1997, 91, 875–879.
  19. Burge, C.B.; Padgett, R.; Sharp, P.A. Evolutionary Fates and Origins of U12-Type Introns. Mol. Cell 1998, 2, 773–785.
  20. Basu, M.K.; Makalowski, W.; Rogozin, I.B.; Koonin, E.V. U12 intron positions are more strongly conserved between animals and plants than U2 intron positions. Biol. Direct 2008, 3, 19.
  21. Turunen, J.J.; Niemelä, E.H.; Verma, B.; Frilander, M.J. The significant other: Splicing by the minor spliceosome. Wiley Interdiscip. Rev. RNA 2012, 4, 61–76.
  22. Yeo, G.W.; Van Nostrand, E.L.; Liang, T.Y. Discovery and Analysis of Evolutionarily Conserved Intronic Splicing Regulatory Elements. PLoS Genet. 2007, 3, e85.
  23. Wu, Q.; Krainer, A.R. AT-AC Pre-mRNA Splicing Mechanisms and Conservation of Minor Introns in Voltage-Gated Ion Channel Genes. Mol. Cell. Biol. 1999, 19, 3225–3236.
  24. Patel, A.A.; McCarthy, M.; Steitz, J.A. The splicing of U12-type introns can be a rate-limiting step in gene expression. EMBO J. 2002, 21, 3804–3815.
  25. Moyer, D.C.; LaRue, E.G.; Hershberger, C.E.; Roy, S.W.; Padgett, R.A. Comprehensive database and evolutionary dynamics of U12-type introns. Nucleic Acids Res. 2020.
  26. Montzka, K.A.; Steitz, J.A. Additional low-abundance human small nuclear ribonucleoproteins: U11, U12, etc. Proc. Natl. Acad. Sci. USA 1988, 85, 8885–8889.
  27. Russell, A.G.; Charette, J.M.; Spencer, D.F.; Gray, M.W. An early evolutionary origin for the minor spliceosome. Nat. Cell Biol. 2006, 443, 863–866.
  28. Rogozin, I.B.; Carmel, L.; Csuros, M.; Koonin, E.V. Origin and evolution of spliceosomal introns. Biol. Direct 2012, 7, 11.
  29. Gilbert, W. The Exon Theory of Genes. Cold Spring Harb. Symp. Quant. Biol. 1987, 52, 901–905.
  30. Dibb, N.J.; Newman, A.J. Evidence that introns arose at proto-splice sites. EMBO J. 1989, 8, 2015–2021.
  31. Dibb, N. Proto-splice site model of intron origin. J. Theor. Biol. 1991, 151, 405–416.
  32. Sverdlov, A.V.; Rogozin, I.B.; Babenko, V.N.; Koonin, E.V. Reconstruction of Ancestral Protosplice Sites. Curr. Biol. 2004, 14, 1505–1508.
  33. Shukla, G.C.; Padgett, R. Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants. RNA 1999, 5, 525–538.
  34. Younis, I.; Dittmar, K.; Wang, W.; Foley, S.W.; Berg, M.G.; Hu, K.Y.; Wei, Z.; Wan, L.; Dreyfuss, G. Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA. eLife 2013, 2, e00780.
  35. Meinke, S.; Goldammer, G.; Weber, A.I.; Tarabykin, V.; Neumann, A.; Preussner, M.; Heyd, F. Srsf10 and the minor spliceosome control tissue-specific and dynamic SR protein expression. eLife 2020, 9, e56075.
  36. Hindorff, L.A.; Sethupathy, P.; Junkins, H.A.; Ramos, E.M.; Mehta, J.P.; Collins, F.S.; Manolio, T.A. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 2009, 106, 9362–9367.
  37. Scotti, M.M.; Swanson, M.S. RNA mis-splicing in disease. Nat. Rev. Genet. 2016, 17, 19–32.
  38. López-Bigas, N.; Audit, B.; Ouzounis, C.; Parra, G.; Guigó, R. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett. 2005, 579, 1900–1903.
  39. Verma, B.; Akinyi, M.; Norppa, A.J.; Frilander, M.J. Minor spliceosome and disease. Semin. Cell Dev. Biol. 2018, 79, 103–112.
  40. Shah, A.A.; Xu, G.; Rosen, A.; Hummers, L.K.; Wigley, F.M.; Elledge, S.J.; Casciola-Rosen, L. Brief Report: Anti–RNPC-3 Antibodies As a Marker of Cancer-Associated Scleroderma. Arthritis Rheumatol. 2017, 69, 1306–1312.
  41. Fischer, D.; Wahlfors, T.; Mattila, H.; Oja, H.; Tammela, T.L.J.; Schleutker, J. MiRNA Profiles in Lymphoblastoid Cell Lines of Finnish Prostate Cancer Families. PLoS ONE 2015, 10, e0127427.
  42. Tian, Y.; Huang, Z.; Wang, Z.; Yin, C.; Zhou, L.; Zhang, L.; Huang, K.; Zhou, H.; Jiang, X.; Li, J.; et al. Identification of Novel Molecular Markers for Prognosis Estimation of Acute Myeloid Leukemia: Over-Expression of PDCD7, FIS1 and Ang2 May Indicate Poor Prognosis in Pretreatment Patients with Acute Myeloid Leukemia. PLoS ONE 2014, 9, e84150.
  43. Lin, C.-F.; Mount, S.M.; Jarmołowski, A.; Makałowski, W. Evolutionary dynamics of U12-type spliceosomal introns. BMC Evol. Biol. 2010, 10, 47.
  44. Dietrich, R.C.; Peris, M.J.; Seyboldt, A.S.; Padgett, R.A. Role of the 3′ Splice Site in U12-Dependent Intron Splicing. Mol. Cell. Biol. 2001, 21, 1942–1952.
  45. Wu, H.-J.; Gaubiercomella, P.; Delseny, M.; Grellet, F.; Van Montagu, M.; Rouze, P. Non–canonical introns are at least 109 years old. Nat. Genet. 1996, 14, 383–384.
  46. Sharp, P.A. Five easy pieces. Science 1991, 254, 663–664.
  47. Lynch, M. The evolution of spliceosomal introns. Curr. Opin. Genet. Dev. 2002, 12, 701–710.
  48. Tarn, W.-Y.; Steitz, J.A. Pre-mRNA splicing: The discovery of a new spliceosome doubles the challenge. Trends Biochem. Sci. 1997, 22, 132–137.
  49. Martin, W.; Koonin, E.V. Introns and the origin of nucleus–cytosol compartmentalization. Nat. Cell Biol. 2006, 440, 41–45.
  50. Schneider, C.; Will, C.L.; Makarova, O.V.; Makarov, E.M.; Lührmann, R. Human U4/U6.U5 and U4atac/U6atac.U5 Tri-snRNPs Exhibit Similar Protein Compositions. Mol. Cell. Biol. 2002, 22, 3219–3229.
  51. Basu, M.K.; Rogozin, I.B.; Koonin, E.V. Primordial spliceosomal introns were probably U2-type. Trends Genet. 2008, 24, 525–528.
  52. Scamborova, P.; Wong, A.; Steitz, J.A. An Intronic Enhancer Regulates Splicing of the Twintron of Drosophila melanogaster prospero Pre-mRNA by Two Different Spliceosomes. Mol. Cell. Biol. 2004, 24, 1855–1869.
  53. Singh, J.; Padgett, R. Rates of in situ transcription and splicing in large human genes. Nat. Struct. Mol. Biol. 2009, 16, 1128–1133.
  54. Wu, Q.; Krainer, A.R. U1-Mediated Exon Definition Interactions between AT-AC and GT-AG Introns. Science 1996, 274, 1005–1008.
  55. Levine, A.; Durbin, R. A computational scan for U12-dependent introns in the human genome sequence. Nucleic Acids Res. 2001, 29, 4006–4013.
  56. Olthof, A.M.; Hyatt, K.C.; Kanadia, R.N. Minor intron splicing revisited: Identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns. BMC Genom. 2019, 20, 686.
  57. Wilkinson, M.E.; Charenton, C.; Nagai, K. RNA Splicing by the Spliceosome. Annu. Rev. Biochem. 2020, 89, 359–388.
  58. Tarn, W.-Y.; Steitz, J.A. Highly Diverged U4 and U6 Small Nuclear RNAs Required for Splicing Rare AT-AC Introns. Science 1996, 273, 1824–1832.
  59. Wassarman, K.M.; Steitz, J.A. The low-abundance U11 and U12 small nuclear ribonucleoproteins (snRNPs) interact to form a two-snRNP complex. Mol. Cell. Biol. 1992, 12, 1276–1285.
  60. Frilander, M.J.; Steitz, J.A. Initial recognition of U12-dependent introns requires both U11/5′ splice-site and U12/branchpoint interactions. Genes Dev. 1999, 13, 851–863.
  61. Will, C.L.; Schneider, C.; Reed, R.; Lührmann, R. Identification of Both Shared and Distinct Proteins in the Major and Minor Spliceosomes. Science 1999, 284, 2003–2005.
  62. Golas, M.M.; Sander, B.; Will, C.L.; Lührmann, R.; Stark, H. Molecular Architecture of the Multiprotein Splicing Factor SF3b. Science 2003, 300, 980–984.
  63. Will, C.L.; Schneider, C.; Hossbach, M.; Urlaub, H.; Rauhut, R.; Elbashir, S.; Tuschl, T.; Lührmann, R. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. RNA 2004, 10, 929–941.
  64. Will, C.L.; Schneider, C.; Macmillan, A.M.; Katopodis, N.F.; Neubauer, C.; Wilms, M.; Lührmann, R.; Query, C.C. A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site. EMBO J. 2001, 20, 4536–4546.
  65. Lorkovic, Z.J.; Lehner, R.; Forstner, C.; Barta, A. Evolutionary conservation of minor U12-type spliceosome between plants and humans. RNA 2005, 11, 1095–1107.
  66. Park, S.J.; Jung, H.J.; Dinh, S.N.; Kang, H. Structural features important for the U12 snRNA binding and minor spliceosome assembly of Arabidopsis U11/U12-small nuclear ribonucleoproteins. RNA Biol. 2016, 13, 670–679.
  67. Nottrott, S.; Hartmuth, K.; Fabrizio, P.; Urlaub, H.; Vidovic, I.; Ficner, R.; Luhrmann, R. Functional interaction of a novel 15.5 kD [U4/U6·U5] tri-snRNP protein with the 5’ stem-loop of U4 snRNA. EMBO J. 1999, 18, 6119–6133.
  68. Frilander, M.J.; Steitz, J.A. Dynamic Exchanges of RNA Interactions Leading to Catalytic Core Formation in the U12-Dependent Spliceosome. Mol. Cell 2001, 7, 217–226.
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