Functional crosstalk between axon enhancers, polypyrimidine tracts and branchpoint sequences

EMBO Journal

Volumn 16, Issue 23, 1997, Pages 7174-7183

  Buvoli, Massimo ^a,b   Mayer, Stephen A ^c   Patton, James G ^d  

^a UNIVERSITY OF COLORADO   (United States)

^b Ist Genet Biochim ed E   (Italy)

^c HARVARD MEDICAL SCHOOL   (United States)

^d NONE

Author keywords

Exon enhancers; Iterative selection; Pre mRNA splicing

Indexed keywords

PYRIMIDINE; RNA; PYRIMIDINE DERIVATIVE; SMALL NUCLEAR RNA; TROPOMYOSIN;

ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; ENHANCER REGION; EXON; GENE SEQUENCE; INTRON; PRIORITY JOURNAL; RNA SPLICING; SPLICEOSOME; ANIMAL; BIOLOGICAL MODEL; CONFORMATION; GENETIC SELECTION; GENETICS; RAT;

ANIMALS; EXONS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; PYRIMIDINES; RATS; RNA SPLICING; RNA, SMALL NUCLEAR; SELECTION (GENETICS); TROPOMYOSIN;

EID: 0031299450     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (77)

1. Abmayr, S.M. Workman, J.L. and Roeder, R.G. (1988) The pseudorabies immediate early protein stimulates in vitro transcription by facilitating TFIID:promoter interactions. Genes Dev., 2, 542-553.
2. Abovich, N. and Rosbash, M. (1997) Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell, 89, 403-412.
3. Adams, M.D., Rudner, D.Z. and Rio, D.R. (1996) Biochemistry and regulation of pre-mRNA splicing. Curr. Opin. Cell Biol., 8, 331-339.
4. Adema, G.J., Bovenberg, R.A.L., Jansz, H.S. and Baas, P.D. (1988) Unusual branchpoint selection involved in splicing of the alternatively processed calcitonin/CGRP-1 pre-mRNA. Nucleic Acids Res., 16, 9513-9525.
5. Coolidge, C.J., Seely, R.J. and Patton, J.G. (1997) Functional analysis of the polypyrimidine tract in pre-mRNA splicing. Nucleic Acids Res., 25, 888-896.
6. Coulter, L.R., Landree, M.A. and Cooper, T.A. (1997) Identification of a new class of exonic splicing enhancers by in vivo selection. Mol. Cell. Biol., 17, 2143-2150.
7. Fu, X.-D. (1993) Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature, 365, 82-85.
8. Fu, X.-D. (1995) The superfamily of arginine/serine-rich splicing factors. RNA, 1, 663-680.
9. Fu, X.-Y., Ge, H. and Manley, J.L. (1988) The role of the polypyrimidine stretch at the SV40 early pre-mRNA 3′ splice site in alternative splicing. EMBO J., 7, 809-817.
10. Hampson, R.K., LaFollette, L. and Rottman, F.M. (1989) Alternative processing of bovine growth hormone mRNA is influenced by downstream exon sequences. Mol. Cell. Biol. 9, 1604-1610.
11. Hartmuth, K. and Barta, A. (1988) Unusual branchpoint slection in processing of human growth hormone pre-mRNA. Mol. Cell. Biol., 8, 2011-2020.
12. Helfman, D., Roscigno, R.F., Mulligan, G.J., Finn, L.A. and Weber, K.S. (1990) Identification of two distinct intron elements involved in alternative splicing of β-tropomyosin pre-mRNA. Genes Dev., 4, 98-110.
13. Hornig, H., Aebi, M. and Weissman, C. (1986) Effect of mutations at the lariat branch acceptor site on β-globin pre-mRNA splicing in vitro. Nature, 324, 589-591.
14. Hoshijima, K., Inoue, K., Higuchi, I. and Shimura, Y. (1991) Control of doublesex alternative splicing by transformer and transformer-2 in Drosophila. Science, 252, 833-836.
15. Humphrey, M.B., Bryan, J., Cooper, T.A. and Berget, S.M. (1995) A 32 nucleotide exon splicing enhancer regulates usage of competing 5′ splice sites in a differential internal exon. Mol. Cell. Biol., 15, 3979-3988.
16. Imai, Y., Matshushima, Y., Sugimura, T. and Terada, M. (1991) A simple and rapid method for generating a deletion by PCR. Nucleic Acids Res., 19, 2785.
17. Jacquier, A. (1990) Self-splicing group II and nuclear pre-mRNA introns: how similar are they? Trends Biochem. Sci., 15, 351-354.
18. Jamison, S.F. and Garcia-Blanco, M.A. (1992) An ATP-independent U2 small nuclear ribonucleoprotein particle/precursor mRNA complex requires both splice sites and the polypyrimidine tract. Proc. Natl Acad. Sci. USA, 89, 5482-5486.
19. Kohtz, J.D., Jamison, S.F., Will, C.L., Zuo, P., Lührmann, R., Garcia-Blanco, M.A. and Manley, J. (1994) Protein-protein interactions and 5′ splice site recognition in mammalian mRNA precursors. Nature, 368, 119-124.
20. Konarska, M.M. and Sharp, P.A. (1986) Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs. Cell, 46, 845-855.
21. Krämer, A. (1996) The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu. Rev. Biochem., 65, 367-409.
22. Lavigueur, A., La Branche, H., Kornblihtt, A.R. and Chabot, B. (1993) A splicing enhancer in the human fibronectin alternate ED1 exon interacts with SR proteins and stimulates U2 snRNP binding. Genes Dev., 7, 2405-2417.
23. Libri, D., Stutz, F., McCarthy, T. and Rosbash, M. (1995) RNA structural patterns and splicing: molecular basis for an RNA-based enhancer. RNA, 1, 425-436.
24. Lin, C.-H. and Patton, J.G. (1995) Regulation of alternative 3′ splice site selection by constitutive splicing factors. RNA, 1, 234-245.
25. Lou, H., Cote, G.J., Berget, S.M. and Gagel, R.F. (1995) An intron enhancer containing a 5′ splice site sequence in the human calcitonin/calcitonin gene-related peptide gene. Mol. Cell. Biol., 15, 7135-7142.
26. Lukashin, A.V., Engelbrecht, J. and Brunak, S. (1992) Multiple alignment using simulated annealing: branchpoint definition in human mRNA splicing. Nucleic Acids Res., 20, 2511-2516.
27. Lynch, K.W. and Maniatis, T. (1996) Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer. Genes Dev., 10, 2089-2101.
28. Madhani, H.D. and Guthrie, C. (1994) Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet., 28, 1-26.
29. Manley, J.L. and Tacke, R. (1996) SR proteins and splicing control. Genes Dev., 10, 1569-1579.
30. McPheeters, D.S. (1996) Interactions of the yeast U6 RNA with the pre-mRNA branch site. RNA, 2, 1110-1123.
31. Michaud, S. and Reed, R. (1991) An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathway. Genes Dev., 5, 2534-2546.
32. Michaud, S. and Reed, R. (1993) A functional association between the 5′ and 3′ splice site is established in the earliest prespliceosome complex (E) in mammals. Genes Dev., 7, 1008-1020.
33. Moore, M.J. and Sharp, P.A. (1992) Site-specific modification of pre-mRNA: the 2′-hydroxyl groups at the splice sites. Science, 256, 992-997.
34. Moore, M.J., Query, C.C. and Sharp, P.A. (1993) Splicing of precursors to mRNA by the spliceosome. In Gesteland, R.F. and Atkins, J.F. (eds), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 303-358.
35. Mount, S.M., Burks, C., Stormo, G.D., White, O. and Fields, C. (1992) Splicing signals in Drosophila: intron size, information content and consensus sequences. Nucleic Acids Res., 20, 4255-4262.
36. Mullen, M.P., Smith, C.W.J., Patton, J.G. and Nadal-Ginard, B. (1991) α-Tropomyosin mutually exclusive exon selection: competition between branchpoint/polypyrimidine tracts determines exon choice. Genes Dev., 5, 642-655.
37. Nilsen, T.W. (1994) RNA-RNA interactions in the spliceosome: unraveling the ties that bind. Cell, 78, 1-4.
38. Norton, P.A. (1994) Polypyrimidine tract sequences direct selection of alternative branch sites and influence protein binding. Nucleic Acids Ref., 22, 3854-3860.
39. Parker, R. and Patterson, B. (1987) Architecture of fungal introns: implications for spliceosome assembly. In Inouye, M. and Dudock, B.S. (eds), Molecular Biology of RNA: New Perspectives. Academic Press, San Diego, CA, pp. 133-149.
40. Parker, R., Siliciano, P.G. and Guthrie, C. (1987) Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. Cell, 49, 229-239.
41. Patterson, B. and Guthrie, C. (1991) A U-rich tract enhances usage of an alternative 3′ splice site in yeast. Cell, 64, 181-187.
42. Query, C.C., Moore, M.J. and Sharp, P.A. (1994) Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model. Genes Dev., 8, 587-597.
43. Query, C.C., Strobel, S.A. and Sharp, P.A. (1996) Three recognition events at the branch-site adenine. EMBO J., 15, 1392-1402.
44. Reed, R. (1989) The organization of 3′ splice-site sequences in mammalian introns. Genes Dev., 3, 2113-2123.
45. Rosbash, M. and Seraphin, B. (1991) Who's on first? The U1 snRNP-5′ splice site interaction and splicing. Trends Biochem Sci., 16, 187-190.
46. Roscigno, R.F., Weiner, M. and Garcia-Blanco, M.A. (1993) A mutational analysis of the polypyrimidine tract of introns: effects of sequence differences in pyrimidine tracts on splicing. J. Biol. Chem., 268, 11222-11229.
47. Ruskin, B. and Green, M.R. (1990) RNA lariat debranching enzyme as tool for analyzing RNA structure. Methods Enzymol., 181, 180-188.
48. Ruskin, B., Greene, J.M. and Green, M.R. (1985) Cryptic branchpoint activation allows accurate in vitro splicing of human β-globin intron mutants. Cell, 41, 833-844.
49. Ruskin, B., Zamore, P.D. and Green, M.R. (1988) A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly. Cell, 52, 207-219.
50. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
51. Schmelzer, C. and Schweyen, R.J. (1986) Self-splicing of Group II introns in vitro: mapping of the branchpoint and mutational analysis of lariat formation. Cell, 46, 557-565.
52. Senepathy, P., Shapiro, M.B. and Harris, N.L. (1990) Splice junctions, branchpoint sites and exons: sequence statistics, identification and application to genome project. Methods Enzymol., 183, 252-278.
53. Singh, R., Valcárcel, J. and Green, M.R. (1995) Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract binding proteins. Science, 268, 1173-1176.
54. Smith, C.W.J. and Nadal-Ginard, B. (1989) Mutually exclusive splicing of α-tropomyosin exons enforced by an unusual lariat branch point location; implications for constitutive splicing. Cell, 56, 749-758.
55. Smith, C.W.J., Patton, J.G. and Nadal-Ginard, B. (1989a) Alternative splicing in the control of gene expression. Annu. Rev. Genet., 23, 527-577.
56. Smith, C.W.J., Porro, E.B., Patton, J.G. and Nadal-Ginard, B. (1989b) Scanning from an independently specified branchpoint defines the 3′ splice site of mammalian introns. Nature, 342, 243-247.
57. Staknis, D. and Reed, R. (1994) SR proteins promote the first specific recognition of pre-mRNA and are present together with the U1 small nuclear ribonucleoprotein particle in a general splicing enhancer complex. Mol. Cell. Biol., 14, 7670-7682.
58. Sun, Q., Mayeda, A., Hampson, R.K., Krainer, A.R. and Rottman, F.M. (1993) General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes Dev., 7, 2598-2608.
59. Tanaka, K., Watakabe, A. and Shimura, Y. (1994) Polypurine sequences within a downstream exon function as a splicing enhancer. Mol. Cell. Biol., 14, 1347-1354.
60. Tarn, W.-Y. and Steitz, J.A. (1995) Modulation of 5′ splice site choice in pre-messenger RNA by two distinct steps. Proc. Natl Acad. Sci. USA, 92, 2504-2508.
61. Tian, H. and Kole, R. (1995) Selection of novel exon recognition elements from a pool of random sequences. Mol. Cell. Biol., 15, 6291-6298.
62. Tian, M. and Maniatis, T. (1994) A splicing enhancer exhibits both constitutive and regulated activities. Genes Dev., 8, 1703-1712.
63. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
64. Valcárcel, J. and Green, M.R. (1996) The SR protein family: pleiotropic functions in pre-mRNA splicing. Trends Biochem Sci., 21, 296-301.
65. Valcárcel, J., Singh, R. and Green, M.R. (1995) Mechanisms of regulated pre-mRNA splicing. In Lamond, A.I. (ed.), Pre-mRNA. Processing. R.G. Landes Co., Austin, TX, pp. 97-112.
66. Watakabe, A., Tanaka, K. and Shimura, Y. (1993) The role of exon sequences in splice site selection. Genes Dev., 7, 407-418.
67. Weiner, A.M. (1993) mRNA splicing and autocatalytic introns: distant cousins or the products of chemical determinism? Cell, 72, 161-164.
68. Wu, J.Y. and Maniatis, T. (1993) Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell, 75, 1061-1070.
69. Wu, J. and Manley, J.L. (1989) Mammalian pre-mRNA branch site selection by U2 snRNP involves base pairing. Genes Dev., 3, 1553-1561.
70. Xu, R., Teng, J. and Cooper, T.A. (1993) The cardiac troponin T alternative exon contains a novel purine-rich positive splicing element. Mol. Cell. Biol., 13, 3660-3674.
71. Yeakley, J.M., Hedjran, F., Morfin, J.-P., Merillat, N., Rosenfeld, M.G. and Emeson, R.B. (1993) Control of calcitonin/calcitonin gene-related peptide pre-mRNA processing by constitutive intron and exon elements. Mol. Cell. Biol., 13, 5999-6011.
72. Yeakley, J.M., Morfin, J.-P., Rosenfeld, M.G. and Fu, X.-D. (1996) A complex of nuclear proteins mediates SR protein binding to a purine-rich splicing enhancer. Proc. Natl Acad. Sci. USA, 93, 7582-7587.
73. Zamore, P.D., Patton, J.G. and Green, M.R. (1992) Cloning and domain structure of the mammalian splicing factor U2AF. Nature. 355, 609-614.
74. Zheng, Z.-M., He, P. and Baker, C.C. (1996) Selection of the bovine papillomavirus type I nucleotide 3225 3′ splice site is regulated through an exonic splicing enhancer and its juxtaposed exonic splicing suppressor. J. Virol., 70, 4691-4699.
75. Zhuang, Y. and Weiner, A.M. (1989) A compensatory base change in human U2 snRNA can suppress a branch site mutation. Genes Dev., 3, 1545-1552.
76. Zhuang, Y., Goldstein, A.M. and Weiner, A.M. (1989) UACUAAC is the preferred branch site for mammalian mRNA splicing. Proc. Natl Acad. Sci. USA, 86, 2752-2756.
77. Zuo, P. and Maniatis, T. (1996) The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. Genes Dev., 10, 1356-1368.