G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection

Molecular and Cellular Biology

Volumn 17, Issue 8, 1997, Pages 4562-4571

  McCullough, Andrew J ^a   Berget, Susan M ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA GLOBIN;

ARTICLE; BINDING SITE; CODON; ENHANCER REGION; GENE MUTATION; HUMAN; HUMAN CELL; INTRON; MOLECULAR RECOGNITION; PRIORITY JOURNAL; RNA SPLICING; SEQUENCE ANALYSIS;

EUKARYOTA; VERTEBRATA;

EID: 0030743391     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.17.8.4562     Document Type: Article

References (53)

1. nrb /NonO. Mol. Cell. Biol. 17:677-686.
2. Berget, S. M. 1995. Exon recognition in vertebrate splicing. J. Biol. Chem. 270:2411-2414.
3. Black, D. L. 1992. Activation of c-src neuron-specific splicing by an unusual RNA element in vivo and in vitro. Cell 69:795-807.
4. Black, D. L. 1995. Finding splice sites within a wilderness of RNA. RNA 1:763-771.
5. Burd, C. G., and G. Dreyfuss. 1994. RNA binding of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing. EMBO J. 13:1197-1204.
6. Caputi, M., G. Casari, S. Guenz, R. Tagliabue, A. Sidoli, C. A. Melo, and F. E. Baralle. 1994. A novel bipartite splicing enhancer modulates the differential processing of the human fibronectin EDA exon. Nucleic Acids Res. 22:1018-1022.
7. Carlo, T., D. A. Sterner, and S. M. Berget. 1996. An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon. RNA 2:342-353.
8. Chabot, B., M. Blanchette, I. Lapierre, and H. La Branche. 1997. An intron element modulating 5′ splice site selection in the hnRNP A1 pre-mRNA interacts with hnRNP A1. Mol. Cell. Biol. 17:1776-1786.
9. Conrad, R., K. Lea, and T. Blumenthal. 1995. SL1 trans-splicing specified by AU-rich synthetic RNA inserted at the 5′ end of Caenorhabditis elegans pre-mRNA. RNA 1:164-170.
10. Crispino, J. D., B. J. Blencowe, and P. A. Sharp. 1994. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1snRNP. Science 265:1866-1869.
11. Dirksen, W. P., R. K. Hampson, S. Qiang, and F. M. Rottman. 1994. A purine-rich exon sequence enhances alternative splicing of bovine growth hormone pre-mRNA. J. Biol. Chem. 269:6431-6436.
12. Engelbrecht, J., S. Knudsen, and S. Brunak. 1992. G+C-rich tract in 5′ end of human introns. J. Mol. Biol. 227:108-113.
13. Goodall, G. J., and W. Filipowicz. 1989. The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 58:473-483.
14. Guo, M., P. C. H. Lo, and S. M. Mount. 1993. Species-specific signals for the splicing of a short Drosophila intron in vitro. Mol. Cell. Biol. 13:1104-1118.
15. Hawkins, J. D. 1988. A survey on intron and exon lengths. Nucleic Acids Res. 16:9893-9908.
16. Huh. G. S., and R. O. Hynes. 1993. Elements regulating an alternatively spliced exon of the rat fibronectin gene. Mol. Cell. Biol. 13:5301-5314.
17. Huh, G. S., and R. O. Hynes. 1994. Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element. Genes Dev. 8:1561-1574.
18. Humphrey, M. B., J. Bryan, T. A. Cooper, and S. M. Berget. 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.
19. Kennedy, C. F., and S. M. Berget. 1997. Pyrimidine tracts between the 5′ splice site and branch point facilitate splicing and recognition of a small Drosophila intron. Mol. Cell. Biol. 17:2774-2780.
20. Lamond, A. I., M. M. Konarska, and P. A. Sharp. 1987. A mutational analysis of spliceosome assembly: evidence for splice site collaboration during spliceosome formation. Genes Dev. 1:532-543.
21. Lavigueur, A., H. La Branche, A. R. Kornblihtt, and B. Chabot. 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.
22. Lou, H., A. J. McCullough, and M. A. Schuler. 1993. 3′ splice site selection in dicot plant nuclei is position dependent. Mol. Cell. Biol. 13:4485-4493.
23. Lou, H., Y. Yang, G. J. Cote, S. M. Berget, and R. F. Gagel. 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.
24. Lou, H., R. F. Gagel, and S. M. Berget. 1996. An intron enhancer recognized by splicing factors activates polyadenylation. Genes Dev. 10:208-219.
25. MacMillan, A. M., P. S. McCaw, J. D. Crispino, and P. A. Sharp. 1997. SC35-mediated reconstitution of splicing in U2AF-depleted nuclear extract. Proc. Natl. Acad. Sci. USA 94:133-136.
26. Matunis, M. J., J. Xing, and G. Dreyfuss. 1994. The hnRNP F protein: unique primary structure, nucleic acid-binding properties, and subcellular localization. Nucleic Acids Res. 22:1059-1067.
27. McCullough, A. J., H. Lou, and M. A. Schuler. 1993. Factors affecting authentic 5′ splice site selection in plant nuclei. Mol. Cell. Biol. 13:1323-1331.
28. McCullough, A. J., and M. A. Schuler. 1993. AU-rich intronic elements affect pre-mRNA 5′ splice site selection in Drosophila melanogaster. Mol. Cell. Biol. 13:7689-7697.
29. McCullough, A. J., C. E. Baynton, and M. A. Schuler. 1996. Interactions across exons can influence splice site recognition in plant nuclei. Plant Cell 8:2295-2307.
30. Min, H., R. C. Chan, and D. L. Black. 1995. The generally expressed hnRNP F is involved in a neural-specific pre-mRNA splicing event. Genes Dev. 9:2659-2671.
31. Mount, S. M., C. Burks, G. Hertz, G. D. Stormo, O. White, and C. Fields. 1992. Splicing signals in Drosophila: intron size, information content and consensus sequences. Nucleic Acids Res. 20:4255-4262.
32. Nakai, K., and H. Sakamoto. 1994. Construction of a novel database containing aberrant splicing mutations of mammalian genes. Gene 141:171-177.
33. Nussinov, R. 1988. Conserved quartets near 5′ intron junctions in primate nuclear pre-mRNA. J. Theor. Biol. 133:73-84.
34. Nussinov, R. 1989. Conserved signals around 5′ splice sites in eukaryotic nuclear precursor RNAs: G-runs are frequent in the introns and C in the exons near both 5′ and 3′ splice sites. J. Biomol. Struct. Dyn. 6:985-1000.
35. Ramchatesingh, J., A. M. Zahler, K. M. Neugebauer, M. B. Roth, and T. A. Cooper. 1995. A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer. Mol. Cell. Biol. 15:4898-4907.
36. Reed, R. 1995. Initial splice site pairing during pre-mRNA splicing. Curr. Opin. Genet. Dev. 6:215-229.
37. Robberson, B. L., G. J. Cote, and S. M. Berget. 1990. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10:84-94.
38. Ryan, K. J., and T. A. Cooper. 1996. Muscle-specific splicing enhancers regulate inclusion of the cardiac troponin T alternative exon in embryonic skeletal muscle. Mol. Cell. Biol. 16:4014-4023.
39. Sirand-Pugnet, P., P. Durosay, E. Brody, and J. Marie. 1995. An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken β-tropomyosin gene. Nucleic Acids Res. 23:3501-3507.
40. Solovyev, V. V., A. A. Salamov, and C. B. Lawrence. 1994. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res. 22:5156-5163.
41. Staknis, D., and R. Reed. 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.
42. Sterner, D. A., T. Carlo, and S. M. Berget. 1996. Architectural limits on split genes. Proc. Natl. Acad. Sci. USA 93:15081-15085.
43. Sun, Q., A. Mayeda, R. K. Hampson, A. R. Krainer, and F. M. Rottman. 1993. General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes Dev. 7:2598-2608.
44. Tacke, R., and J. L. Manley. 1995. The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J. 14:3540-3551.
45. Tacke, R., and J. L. Manley. 1997. Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: creation of an SRp40-specific splicing enhancer. Proc. Natl. Acad. Sci. USA 94:1148-1153.
46. Talerico, M., and S. M. Berget. 1990. Effect of 5′ splice site mutations on splicing of the preceding intron. Mol. Cell. Biol. 10:6299-6305.
47. Talerico, M., and S. M. Berget. 1993. Intron definition in splicing of small Drosophila introns. Mol. Cell. Biol. 14:3434-3445.
48. Tanaka, K., A. Watakabe, and Y. Shimura. 1994. Polypurine sequences within a downstream exon function as a splicing enhancer. Mol. Cell. Biol. 14:1347-1354.
49. Tarn, W. Y., and J. A. Steitz. 1994. SR proteins can compensate for the loss of U1snRNP functions in vitro. Genes Dev. 8:2707-2717.
50. Watakabe, A., K. Tanaka, and Y. Shimura. 1993. The role of exon sequences in splice site selection. Genes Dev. 7:407-418.
51. Wise, J. A. Personal communication.
52. Xu, R., J. Teng, and T. A. Cooper. 1993. The cardiac troponin T alternative exon contains a novel purine-rich positive splicing element. Mol. Cell. Biol. 13:3660-3674.
53. Yeakley, J. M., F. Hedjran, J.-P. Morfin, N. Merillat, M. G. Rosenfeld, and R. B. Emeson. 1993. Control of calcitonin/calcitonin gene-related peptide pre-mRNA processing by constitutive exon and intron elements. Mol. Cell. Biol. 13:5999-6011.