Determinants of the inherent strength of human 5′ splice sites

RNA

Volumn 11, Issue 5, 2005, Pages 683-698

  Roca, Xavier ^a   Sachidanandam, Ravi ^a   Krainer, Adrian R ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

5 splice site; pre mRNA splicing; Pseudouridine; U1 snRNA

Indexed keywords

BETA GLOBIN; MESSENGER RNA;

ARTICLE; ENERGY TRANSFER; EXON; GENE MUTATION; GENE SEQUENCE; HUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA SPLICING; WILD TYPE;

ALTERNATIVE SPLICING; BASE PAIRING; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; EXONS; GLOBINS; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; MUTATION; RNA PRECURSORS; RNA SPLICE SITES; RNA SPLICING; RNA, SMALL NUCLEAR; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 17844367842     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2040605     Document Type: Article

References (73)

1. Alvarez, C.J. and Wise, J.A. 2001. Activation of a cryptic 5′ splice site by U1 snRNA. RNA 7: 342-350.
2. Arnez, J.G. and Steitz, T.A. 1994. Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. Biochemistry 33: 7560-7567.
3. Brackenridge, S., Wilkie, A.O., and Screaton, G.R. 2003. Efficient use of a 'dead-end' GA 5′ splice site in the human fibroblast growth factor receptor genes. EMBO J. 22: 1620-1631.
4. Brow, D.A. 2002. Allosteric cascade of spliceosome activation. Annu. Rev. Genet. 36: 333-360.
5. Brunak, S., Engelbrecht, J., and Knudsen, S. 1991. Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol. 220: 49-65.
6. Buchner, D.A., Trudeau, M., and Meisler, M.H. 2003. SCNM1, a putative RNA splicing factor that modifies disease severity in mice. Science 301: 967-969.
7. Buratti, E., Baralle, M., De Conti, L., Baralle, D., Romano, M., Ayala, Y.M., and Baralle, F.E. 2004. hnRNP H binding at the 5′ splice site correlates with the pathological effect of two intronic mutations in the NF-1 and TSHβ genes. Nucleic Acids Res. 32: 4224-4236.
8. Burge, C. 1998. Modeling dependencies in pre-mRNA splicing signals. In Computational methods in molecular biology (eds. S.L. Salzberg et al.), chapter 8, pp. 129-164. Elsevier Science, Philadelphia, PA.
9. Cáceres, J.F., Stamm, S., Helfman, D.M., and Krainer, A.R. 1994. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science 265: 1706-1709.
10. Cai, D., Delcher, A., Kao, B., and Kasif, S. 2000. Modeling splice sites with Bayes networks. Bioinformatics 16: 152-158.
11. Cartegni, L., Chew, S.L., and Krainer, A.R. 2002. Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat. Rev. Genet. 3: 285-298.
12. Chabot, B. and Steitz, J.A. 1987. Recognition of mutant and cryptic 5′ splice sites by the U1 small nuclear ribonucleoprotein in vitro. Mol. Cell. Biol. 7: 698-707.
13. Chen, X., McDowell, J.A., Kierzek, R., Krugh, T.R., and Turner, D.H. 2000. Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G·U pairs: One hydrogen bond for each G·U pair in r(GGCGUGCC)(2) and two for each G·U pair in r(GAGUGCUC)(2). Biochemistry 39: 8970-8982.
14. Chen, J.Y., Stands, L., Staley, J.P., Jackups, R.R.J., Latus, L.J., and Chang, T.H. 2001. Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor. Mol. Cell 7: 227-232.
15. Collins, C.A. and Guthrie, C. 1999. Allele-specific genetic interactions between Prp8 and RNA active site residues suggest a function for Prp8 at the catalytic core of the spliceosome. Genes & Dev. 13: 1970-1982.
16. Cortes, J.J., Sontheimer, E.J., Seiwert, S.D., and Steitz, J.A. 1993. Mutations in the conserved loop of human U5 snRNA generate use of novel cryptic 5′ splice sites in vivo. EMBO J. 12: 5181-5189.
17. Crispino, J. and Sharp, P. 1995. A U6 snRNA:pre-mRNA interaction can be rate-limiting for U1-independent splicing. Genes & Dev. 9: 2314-2323.
18. Crispino, J.D., Blencowe, B.J., and Sharp, P.A. 1994. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. Science 265: 1866-1869.
19. Cunningham, S.A., Else, A.J., Potter, B.V., and Eperon, I.C. 1991. Influences of separation and adjacent sequences on the use of alternative 5′ splice sites. J. Mol. Biol. 217: 265-281.
20. Davis, D.R. 1995. Stabilization of RNA stacking by pseudouridine. Nucleic Acids Res. 23: 5020-5026.
21. Du, H. and Rosbash, M. 2001. Yeast U1 snRNP-pre-mRNA complex formation without U1snRNA-pre-mRNA base pairing. RNA 7: 133-142.
22. _. 2002. The U1 snRNP protein U1C recognizes the 5′ splice site in the absence of base pairing. Nature 419: 86-90.
23. Eperon, L.P., Estibeiro, J.P., and Eperon, I.C. 1986. The role of nucleotide sequences in splice site selection in eukaryotic pre-messenger RNA. Nature 324: 280-282.
24. Eperon, I.C., Ireland, D.C., Smith, R.A., Mayeda, A., and Krainer, A.R. 1993. Pathways for selection of 5′ splice sites by U1 snRNPs and SF2/ASF. EMBO J. 12: 3607-3617.
25. Eperon, I.C., Makarova, O.V., Mayeda, A., Munroe, S.H., Cáceres, J.F., Hayward, D.G., and Krainer, A.R. 2000. Selection of alternative 5′ splice sites: Role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1. Mol. Cell Biol. 20: 8303-8318.
26. Forch, P., Puig, O., Martinez, C., Séraphin, B., and Valcárcel, J. 2002. The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5′ splice sites. EMBO J. 21: 6882-6892.
27. Freund, M., Asang, C., Kammler, S., Konermann, C., Krummheuer, J., Hipp, M., Meyer, I., Gierling, W., Theiss, S., Preuss, T., et al. 2003. A novel approach to describe a U1 snRNA binding site. Nucleic Acids Res. 31: 6963-6975.
28. Hall, K.B. and McLaughlin, L.W. 1991. Properties of a U1/mRNA 5′ splice site duplex containing pseudouridine as measured by thermodynamic and NMR methods. Biochemistry 30: 1795-1801.
29. Horowitz, D.S. and Krainer, A.R. 1994. Mechanisms for selecting 5′ splice sites in mammalian pre-mRNA splicing. Trends Genet. 10: 100-106.
30. Hwang, D.Y. and Cohen, J.B. 1996. U1 snRNA promotes the selection of nearby 5′ splice sites by U6 snRNA in mammalian cells. Genes & Dev. 10: 338-350.
31. Kandels-Lewis, S. and Séraphin, B. 1993. Involvement of U6 snRNA in 5′ splice site selection. Science 262: 2035-2039.
32. Krainer, A.R., Maniatis, T., Ruskin, B., and Green, M.R. 1984. Normal and mutant human β-globin pre-mRNAs are faithfully and efficiently spliced in vitro. Cell 36: 993-1005.
33. Krainer, A.R., Conway, G.C., and Kozak, D. 1990. The essential pre-mRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites. Cell 62: 35-42.
34. Ladd, A.N. and Cooper, T.A. 2002. Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol. 3: reviews0008.1-0008.16.
35. Lear, A.L., Eperon, L.P., Wheatley, I.M., and Eperon, I.C. 1990. Hierarchy for 5′ splice site preference determined in vivo. J. Mol. Biol. 211: 103-115.
36. Leontis, N.B. and Westhof, E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512.
37. Lesser, C.F. and Guthrie, C. 1993. Mutations in U6 snRNA that alter splice site specificity: Implications for the active site. Science 262: 1982-1988.
38. Libri, D., Ducongé, F., Levy, L., and Vinauger, M. 2002. A role for the ψ-U mismatch in the recognition of the 5′ splice site of yeast introns by the U1 small nuclear ribonucleoprotein particle. J. Biol. Chem. 277: 18173-18181.
39. Lund, M. and Kjems, J. 2002. Defining a 5′ splice site by functional selection in the presence and absence of U1 snRNA 5′ end. RNA 8: 166-179.
40. Maroney, P.A., Romfo, C.M., and Nilsen, T.W. 2000. Functional recognition of 5′ splice site by U4/U6.U5 tri-snRNP defines a novel ATP-dependent step in early spliceosome assembly. Mol. Cell 6: 317-328.
41. Mayeda, A. and Krainer, A.R. 1992. Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell 68: 365-375.
42. _. 1999a. Mammalian in vitro splicing assays. Methods Mol. Biol. 118: 315-321.
43. _. 1999b. Preparation of HeLa cell nuclear and cytosolic S100 extracts for in vitro splicing. Methods Mol. Biol. 118: 309-314.
44. Mayeda, A. and Ohshima, Y. 1988. Short donor site sequences inserted within the intron of β-globin pre-mRNA serve for splicing in vitro. Mol. Cell. Biol. 8: 4484-4491.
45. McCullough, A. and Berget, S. 1997. G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol. Cell. Biol. 17: 4562-4571.
46. _. 2000. An intronic splicing enhancer binds U1 snRNPs to enhance splicing and select 5′ splice sites. Mol. Cell. Biol. 20: 9225-9235.
47. Nelson, K.K. and Green, M.R. 1988. Splice site selection and ribonucleoprotein complex assembly during in vitro pre-mRNA splicing. Genes & Dev. 2: 319-329.
48. Newman, A.J. 1997. The role of U5 snRNP in pre-mRNA splicing. EMBO J. 16: 5797-5800.
49. Newman, A. and Norman, C. 1992. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68: 743-754.
50. O'Keefe, R.T., Norman, C., and Newman, A.J. 1996. The invariant U5 snRNA loop 1 sequence is dispensable for the first catalytic step of pre-mRNA splicing in yeast. Cell 86: 679-689.
51. Ofengand, J. and Bakin, A. 1997. Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J. Mol. Biol. 266: 246-268.
52. Reddy, R., Henning, D., and Busch, H. 1981. Pseudouridine residues in the 5′-terminus of uridine-rich nuclear RNA I (U1 RNA). Biochem. Biophys. Res. Commun. 98: 1076-1083.
53. Reyes, J.L., Kois, P., Konforti, B.B., and Konarska, M.M. 1996. The canonical GU dinucleotide at the 5′ splice site is recognized by p220 of the U5 snRNP within the spliceosome. RNA 2: 213-225.
54. Roca, X., Sachidanandam, R., and Krainer, A.R. 2003. Intrinsic differences between authentic and cryptic 5′ splice sites. Nucleic Acids Res. 31: 6321-6333.
55. Roller, A., Hoffman, D., and Zahler, A. 2000. The allele-specific suppressor sup-39 alters use of cryptic splice sites in Caenorhabditis elegans. Genetics 154: 1169-1179.
56. Senapathy, P., Shapiro, M.B., and Harris, N.L. 1990. Splice junctions, branch point sites, and exons: Sequence statistics, identification, and applications to genome project. Methods Enzymol. 183: 252-278.
57. Séraphin, B., Kretzner, L., and Rosbash, M. 1988. A U1 snRNA:pre-mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5′ cleavage site. EMBO J. 7: 2533-2538.
58. Serra, M.J. and Turner, D.H. 1995. Predicting thermodynamic properties of RNA. Methods Enzymol. 259: 242-261.
59. Shapiro, M.B. and Senapathy, P. 1987. RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression. Nucleic Acids Res. 15: 7155-7174.
60. Siatecka, M., Reyes, J.L., and Konarska, M.M. 1999. Functional interactions of Prp8 with both splice sites at the spliceosomal catalytic center. Genes & Dev. 13: 1983-1993.
61. Siliciano, P.G. and Guthrie, C. 1988. 5′ Splice site selection in yeast: Genetic alterations in base-pairing with U1 reveal additional requirements. Genes & Dev. 2: 1258-1267.
62. Sorek, R., Lev-Maor, G., Reznik, M., Dagan, T., Belinky, F., Graur, D., and Ast, G. 2004. Minimal conditions for exonization of intronic sequences: 5′ Splice site formation in Alu exons. Mol. Cell 14: 221-231.
63. Staley, J. and Guthrie, C. 1999. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell 3: 55-64.
64. Sun, H. and Chasin, L.A. 2000. Multiple splicing defects in an intronic false exon. Mol. Cell. Biol. 20: 6414-6425.
65. Tarn, W. and Steitz, J. 1994. SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes & Dev. 8: 2704-2717.
66. Thanaraj, T.A. 2000. Positional characterisation of false positives from computational prediction of human splice sites. Nucleic Acids Res. 28: 744-754.
67. Treisman, R., Orkin, S.H., and Maniatis, T. 1983. Specific transcription and RNA splicing defects in five cloned β-thalassaemia genes. Nature 302: 591-596.
68. Varani, G. and McClain, W.H. 2000. The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep. 1: 18-23.
69. Wassarman, D.A. and Steitz, J.A. 1992. Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicing. Science 257: 1918-1925.
70. Wyatt, J.R., Sontheimer, E.J., and Steitz, J.A. 1992. Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing. Genes & Dev. 6: 2542-2553.
71. Yeo, G. and Burge, C.B. 2003. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. In Proceedings of the 7th Annual International Conference on Computational Molecular Biology (RECOMB03) (eds. W. Miller et al.), pp. 322-331. ACM Press, New York.
72. Zhang, D. and Rosbash, M. 1999. Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex. Genes & Dev. 13: 581-592.
73. Zhuang, Y. and Weiner, A.M. 1986. A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation. Cell 46: 827-835.