Base pairing at the 5′ splice site with U1 small nuclear RNA promotes splicing of the upstream intron but may be dispensable for splicing of the downstream intron

Molecular and Cellular Biology

Volumn 16, Issue 6, 1996, Pages 3012-3022

  Hwang, Dong Youn ^a   Cohen, Justus B ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEASE S1; SMALL NUCLEAR RNA;

ARTICLE; BASE PAIRING; DNA FLANKING REGION; ENHANCER REGION; EXON; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; INTRON; POINT MUTATION; PRIORITY JOURNAL; RNA SPLICING;

ALTERNATIVE SPLICING; BASE COMPOSITION; BASE SEQUENCE; CELL LINE; ENHANCER ELEMENTS (GENETICS); EXONS; GENES, REPORTER; HELA CELLS; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; OLIGODEOXYRIBONUCLEOTIDES; POINT MUTATION; RNA PRECURSORS; RNA SPLICING; RNA, SMALL NUCLEAR; SUPPRESSION, GENETIC; TRANSFECTION;

MAMMALIA;

EID: 0029982346     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/mcb.16.6.3012     Document Type: Article

References (54)

1. Aebi, M., H. Hornig, and C. Weissmann. 1987. 5′ cleavage site in eukaryotic pre-mRNA splicing is determined by the overall 5′ splice region, not by the conserved 5′ GU. Cell 50:237-246.
2. Berget, S. M. 1995. Exon recognition in vertebrate splicing. J. Biol. Chem. 270:2411-2414.
3. Cáceres, J. F., S. Stamm, D. M. Helfman, and A. R. Krainer. 1994. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science 265:1706-1709.
4. Cohen, J. B., S. D. Broz, and A. D. Levinson. 1989. Expression of the H-ras proto-oncogene is controlled by alternative splicing. Cell 58:461-472.
5. Cohen, J. B., S. D. Broz, and A. D. Levinson. 1993. U1 small nuclear RNAs with altered specificity can he stably expressed in mammalian cells and promote permanent changes in pre-mRNA splicing. Mol. Cell. Biol. 13:2666-2676.
6. Cohen, J. B., and A. D. Levinson. 1988. A point mutation in the last intron responsible for increased expression and transforming activity of the c-Ha-ras oncogene. Nature (London) 334:119-124.
7. Cohen, J. B., J. E. Snow, S. D. Spencer, and A. D. Levinson. 1994. Suppression of mammalian 5′ splice site defects by U1 small nuclear RNAs from a distance. Proc. Natl. Acad. Sci. USA 91:10470-10474.
8. Cortes, J. J., E. J. Sontheimer, S. D. Seiwert, and J. A. Steitz. 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.
9. Crispino, J. D., B. J. Blencowe, and P. A. Sharp. 1994. Complementation by SR proteins of pre-mRN A splicing reactions depleted of U1 snRNP. Science 265:1866-1869.
10. Dominski, Z., and R. Kole. 1991. Selection of splice sites in pre-mRNAs with short internal exons. Mol. Cell. Biol. 11:6075-6083.
11. 65 and a novel spliceosome-associated 28-kDa protein. RNA 1:407-417.
12. Ge, H., and J. L. Manley. 1990. A protein factor, ASF. controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell 62:25-34.
13. Green, M. R. 1991. Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Annu. Rev. Cell Biol. 7:559-599.
14. Hampson, R. K., L. La Follette, and F. M. Rottman. 1989. Alternative processing of bovine growth hormone mRNA is influenced by downstream exon sequences. Mol. Cell. Biol. 9:1604-1610.
15. Hoffman, B. E., and P. J. Grabowski. 1992. U1 snRNP targets an essential splicing factor. U2AF65, to the 3′ splice site by a network of interactions spanning the exon. Genes Dev. 6:2554-2568.
16. Hosijima, K., K. Inoue, I. Higuchi, H. Sakamoto, and Y. Shimura. 1991. Control of doublesex alternative splicing by transformer and transformer-2 in Drosophila. Science 252:833-836.
17. Hwang, D.-Y., and J. B. Cohen. 1996. U1 snRNA promotes the selection of nearby 5′ splice sites by U6 snRNA in mammalian cells. Genes Dev. 10:338-350.
18. Kandels-Lewis, S., and B. Séraphin. 1993. Role of U6 snRNA in 5′ splice site selection. Science 262:2035-2039.
19. Kohtz, J. D., S. F. Jamison, C. L. Will, P. Zuo, R. Lührmann, M. A. Garcia-Blanco, and J. L. Manley. 1994. Protein-protein interactions and 5′-splice-site recognition in mammalian mRNA precursors. Nature (London) 368:119-124.
20. Kuo, H., F. H. Nasim, and P. J. Grabowski. 1991. Control of alternative splicing by the differential binding of U1 small nuclear ribonucleoprotein particle. Science 251:1045-1050.
21. Lavigueur, A., H. La Branche, A. R. Kornblihtt, and B. Chabot. 1993. A splicing enhancer in the human fibronectin alternate EDI exon interacts with SR proteins and stimulates U2 snRNP binding. Genes Dev. 7:2405-2417.
22. Lesser, C. M., and C. Guthrie. 1993. Mutations in U6 snRNA that alter splice site specificity: implications for the active site. Science 262:1982-1988.
23. Madhani, H. D., and C. Guthrie. 1994. Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet. 28:1-26.
24. Mayeda, A., D. M. Helfman, and A. R. Krainer. 1993. Modulation of exon skipping and inclusion by heterogeneous nuclear ribonucleoprotein A1 and pre-mRNA splicing factor SF2/ASF. Mol. Cell. Biol 13:2993-3001.
25. Moore, M. J., C. C. Query, and P. A. Sharp. 1993. Splicing of precursors to mRNA by the spliceosome, p. 303-357. In R. F. Gesteland and J. F. Atkins (ed.), The RNA world. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
26. Nagoshi, R. N., and B. S. Baker. 1990. Regulation of sex-specific RNA splicing at the Drosophila doublesex gene: cis-acting mutations in exon sequences alter sex-specific RNA splicing patterns. Genes Dev. 4:89-97.
27. Newman, A. J., and C. Norman. 1991. Mutations in yeast US snRNA alter the specificity of 5′ splice-site cleavage. Cell 65:115-123.
28. Newman, A. J., and C. Norman. 1992. US snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68:743-754.
29. 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.
30. 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.
31. Rosbash, M., and B. Séraphin. 1991. Who's on first? The U1 snRNP-5′ splice site interaction and splicing. Trends Biochem. Sci. 16:187-190.
32. Rymond, B. C., and M. Rosbash. 1992. Yeast pre-mRNA splicing, p. 143-112. In E. W. Jones, J. R. Pringle, and J. R. Broach (ed.), The molecular and cellular biology of the yeast Saccharomyces. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
33. Sawa, H., and Y. Shimura. 1992. Association of U6 snRNA with the 5′-splice site region of pre-mRNA in the spliceosome. Genes Dev. 6:244-254.
34. Séraphin, B., L. Kretzner, and M. Rosbash. 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.
35. Séraphin, B., and M. Rosbash. 1990. Exon mutations uncouple 5′ splice site selection from U1 snRNA pairing. Cell 63:619-629.
36. Siliciano, P. G., and C. Guthrie. 1988. 5′ splice site selection in yeast: genetic alterations in base-pairing with U1 reveal additional requirements. Genes Dev. 2:1258-1267.
37. Smith, C. W. J., E. B. Porro, J. G. Patton, and B. Nadal-Ginard. 1989. Scanning from an independently specified branch point defines the 3′ splice site of mammalian introns. Nature (London) 342:243-247.
38. Sontheimer, E. J., and J. A. Steitz. 1993. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262:1989-1996.
39. 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.
40. Strijker, R., D. T. Fritz, and A. D. Levinson. 1989. Adenovirus VAI-RNA regulates gene expression by controlling stability of ribosome-bound RNAs. EMBO J. 8:2669-2675.
41. 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.
42. Tarn, W.-Y., and J. A. Steitz. 1994. SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes Dev. 8:2704-2717.
43. Tian, M., and T. Maniatis. 1992. Positive control of pre-mRNA splicing in vitro. Science 256:237-240.
44. Tian, M., and T. Maniatis. 1993. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell 74:105-114.
45. van Oers, C. C. M., G. J. Adema, H. Zandberg, T. C. Moen, and P. D. Baas. 1994. Two different sequence elements within exon 4 are necessary for calcitonin-specific splicing of the human calcitonin/calcitonin gene-related peptide I pre-mRNA. Mol. Cell. Biol. 14:951-960.
46. Vieira, J., and J. Messing. 1987. Production of single-stranded plasmid DNA. Methods Enzymol. 153:3-11.
47. Wassarman, D. A., and J. A. Steitz. 1992. Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicing. Science 257:1918-1925.
48. Watakabe, A., K. Tanaka, and Y. Shimura. 1993. The role of exon sequences in splice site selection. Genes Dev. 7:407-418.
49. Woolford, J. L. 1989. Nuclear pre-mRNA splicing in yeast. Yeast 5:439-457.
50. Wu, J. Y., and T. Maniatis. 1493. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75:1061-1070.
51. Wyatt, J. R., E. J. Sontheimer, and J. A. Steitz. 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.
52. Xu, R., J. Teng, and T. A. Cooper. 1993. The cardiac troponin T alternative exon contains a novel purine-rich splicing element. Mol. Cell. Biol. 13:3660-3674.
53. Zahler, A. M., W. S. Lane, J. A. Stolk, and M. B. Roth. 1992. SR proteins: a conserved family of pre-mRNA splicing factors. Genes Dev. 6:837-847.
54. Zuo, P., and J. L. Manley. 1994. The human splicing factor ASF/SF2 can specifically recognize pre-mRNA 5′ splice sites. Proc. Natl. Acad. Sci. USA 91:3363-3357.