Purine-rich enhancers function in the AT-AC pre-mRNA splicing pathway and do so independently of intact U1 snRNP

RNA

Volumn 4, Issue 12, 1998, Pages 1664-1673

  Wu, Qiang ^b   Krainer, Adrian R ^a  

^a Watson School of Biological Sciences   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

AT AC intron; Exon definition; Exonic splicing enhancer (ESE); Pre mRNA splicing; U1 snRNP

Indexed keywords

PURINE;

ALTERNATIVE RNA SPLICING; ARTICLE; BASE PAIRING; CATALYSIS; CROSS LINKING; ENHANCER REGION; EXON; MESSENGER RNA SYNTHESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; SILENCER GENE; SPLICEOSOME;

BASE SEQUENCE; ENHANCER ELEMENTS (GENETICS); EXONS; PURINES; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; RNA, SMALL NUCLEAR;

EUKARYOTA;

EID: 0031730213     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838298981432     Document Type: Article

References (68)

1. Achsel T, Shimura Y. 1996. Factors involved in the activation of pre-mRNA splicing from downstream splicing enhancers. J Biochem (Tokyo) 120:53-60.
2. Amendt BA, Si ZH, Stoltzfus CM. 1995. Presence of exon splicing silencers within human immunodeficiency virus type 1 tat exon 2 and tat-rev exon 3: Evidence for inhibition mediated by cellular factors. Mol Cell Biol 15:4606-4615.
3. Barabino SM, Blencowe BJ, Ryder U, Sproat BS, Lamond AI. 1990. Targeted snRNP depletion reveals an additional role for mammalian U1 snRNP in spliceosome assembly. Cell 63:293-302.
4. Berget SM. 1995. Exon recognition in vertebrate splicing. J Biol Chem 270:2411-2414.
5. Black DL. 1995. Finding splice sites within a wilderness of RNA. RNA 1:763-771.
6. Bruzik JP, Maniatis T. 1995. Enhancer-dependent interaction between 5′ and 3′ splice sites in trans. Proc Natl Acad Sci USA 92:7056-7059.
7. Bruzik JP, Steitz JA. 1990. Spliced leader RNA sequences can substitute for the essential 5′ end of U1 RNA during splicing in a mammalian in vitro system. Cell 62:889-899.
8. Cáceres JF, Krainer AR. 1997. Mammalian pre-mRNA splicing factors. In: Krainer AR. ed. Eukaryotic mRNA processing. Oxford, UK: IRL Press. pp 174-212.
9. Chiara MD, Reed R. 1995. A two-step mechanism for 5′ and 3′ splice-site pairing. Nature 375:510-513.
10. Coulter LR, Landree MA, Cooper TA. 1997. Identification of a new class of exonic splicing enhancers by in vivo selection. Mol Cell Biol 17:2143-2150.
11. Crispino JD, Blencowe BJ, Sharp PA. 1994. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. Science 265:1866-1869.
12. Crispino JD, Sharp PA. 1995. A U6 snRNA: Pre-mRNA interaction can be rate-limiting for U1-independent splicing. Genes & Dev 9:2314-2323.
13. Eperon IC, Ireland DC, Smith RA, Mayeda A, Krainer AR. 1993. Pathways for selection of 5′ splice sites by U1 snRNPs and SF2/ ASF. EMBO J 12:3607-3617.
14. Fu XD, Katz RA, Skalka AM, Maniatis T. 1991. The role of branch-point and 3′-exon sequences in the control of balanced splicing of avian retrovirus RNA. Genes & Dev 5:211-220.
15. Furth PA, Choe WT, Rex JH, Byrne JC, Baker CC. 1994. Sequences homologous to 5′ splice sites are required for the inhibitory activity of papillomavirus late 3′ untranslated regions. Mol Cell Biol 14:5278-5289.
16. Gontarek RR, Derse D. 1996. Interactions among SR proteins, an exonic splicing enhancer, and a lentivirus Rev protein regulate alternative splicing. Mol Cell Biol 16:2325-2331.
17. Hall SL, Padgett RA. 1994. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. J Mol Biol 239:357-365.
18. Hall SL, Padgett RA. 1996. Requirement of U12 snRNA for in vivo splicing of a minor class of eukaryotic nuclear pre-mRNA introns. Science 271:1716-1718.
19. Helfman DM, Ricci WM, Finn LA. 1988. Alternative splicing of tropomyosin pre-mRNAs in vitro and in vivo. Genes & Dev 2:1627-1638.
20. Hertel KJ, Lynch KW, Maniatis T. 1997. Common themes in the function of transcription and splicing enhancers. Curr Opin Cell Biol 9:350-357.
21. Humphrey MB, Bryan J, Cooper TA, Berget SM. 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.
22. Hwang DY, Cohen JB. 1996. U1 snRNA promotes the selection of nearby 5′ splice sites by U6 snRNA in mammalian cells. Genes & Dev 10:338-350.
23. Incorvaia R, Padgett RA. 1998. Base pairing with U6atac snRNA is required for 5′ splice site activation of U12-dependent introns in vivo. RNA 4:709-718.
24. Jackson IJ. 1991. A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res 19:3795-3798.
25. Katz RA, Skalka AM. 1990. Control of retroviral RNA splicing through maintenance of suboptimal processing signals. Mol Cell Biol 10:696-704.
26. Kohtz JD, Jamison SF, Will CL, Zuo P, Lührmann R, Garcia-Blanco MA, Manley JL. 1994. Protein-protein interactions and 5′-splice-site recognition in mammalian mRNA precursors. Nature 368:119-124.
27. Kolossova I, Padgett RA. 1997. U11 snRNA interacts in vivo with the 5′ splice site of U12-dependent (AU-AC) pre-mRNA introns. RNA 3:227-233.
28. Konarska MM, Sharp PA. 1987. Interactions between small nuclear ribonucleoprotein particles in formation of spliceosomes. Cell 49:763-774.
29. Kuo HC, Nasim FH, Grabowski PJ. 1991. Control of alternative splicing by the differential binding of U1 small nuclear ribonucleoprotein particle. Science 251:1045-1050.
30. Lavigueur A, La Branche H, Kornblihtt AR, 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.
31. Lerner MR, Boyle JA, Mount SM, Wolin SL, Steitz JA. 1980. Are snRNPs involved in splicing? Nature 283:220-224.
32. Liu HX, Zhang M, Krainer AR. 1998. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes & Dev 12:1998-2012.
33. Lou H, Gagel RF, Berget SM. 1996. An intron enhancer recognized by splicing factors activates polyadenylation. Genes & Dev 10:208-219.
34. Lynch KW, Maniatis T. 1995. Synergistic interactions between two distinct elements of a regulated splicing enhancer. Genes & Dev 9:284-293.
35. Manley JL, Tacke R. 1996. SR proteins and splicing control. Genes & Dev 10:1569-1579.
36. Mardon HJ, Sebastio G, Baralle FE. 1987. A role for exon sequences in alternative splicing of the human fibronectin gene. Nucleic Acids Res 15:7725-7733.
37. Nilsen TW. 1996. A parallel spliceosome. Science 273:1813.
38. Nilsen TW. 1998. RNA-RNA interactions in nuclear pre-mRNA splicing. In: Simons RW, Grunberg-Manago M. eds. RNA structure and function. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. pp 279-307.
39. Ramchatesingh J, Zahler AM, Neugebauer KM, Roth MB, Cooper TA. 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.
40. Robberson BL, Cote GJ, Berget SM. 1990. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol Cell Biol 10:84-94.
41. Seiwert SD, Steitz JA. 1993. Uncoupling two functions of the U1 small nuclear ribonucleoprotein particle during in vitro splicing. Mol Cell Biol 13:3134-3145.
42. Sharp PA, Burge CB. 1997. Classification of introns: U2-type or U12-type. Cell 91:875-879.
43. Staffa A, Cochrane A. 1995. Identification of positive and negative splicing regulatory elements within the terminal tat-rev exon of human immunodeficiency virus type 1. Mol Cell Biol 15:4597-4605.
44. Staknis D, 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.
45. Stark JM, Bazett-Jones DP, Herfort M, Roth MB. 1998. SR proteins are sufficient for exon bridging across an intron. Proc Natl Acad Sci USA 95:2163-2168.
46. Steingrimsdottir H, Rowley G, Dorado G, Cole J, Lehmann AR. 1992. Mutations which alter splicing in the human hypoxanthine-guanine phosphoribosyltransferase gene. Nucleic Acids Res 20:1201-1208.
47. Sun Q, Mayeda A, Hampson RK, Krainer AR, Rottman FM. 1993. General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes & Dev 7:2598-2608.
48. Tacke R, Manley JL. 1995. The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J 14:3540-3551.
49. Tanaka K, Watakabe A, Shimura Y. 1994. Polypurine sequences within a downstream exon function as a splicing enhancer. Mol Cell Biol 14:1347-1354.
50. Tarn WY, Steitz JA. 1994. SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes & Dev 8:2704-2717.
51. Tarn WY, Steitz JA. 1996a. A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro. Cell 84:801-811.
52. Tarn WY, Steitz JA. 1996b. Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns. Science 273:1824-1832.
53. Tarn WY, Steitz JA. 1997. Pre-mRNA splicing: The discovery of a new spliceosome doubles the challenge. Trends Biochem Sci 22:132-137.
54. Tian H, Kole R. 1995. Selection of novel exon recognition elements from a pool of random sequences. Mol Cell Biol 15:6291-6298.
55. Tian M, Maniatis T. 1994. A splicing enhancer exhibits both constitutive and regulated activities. Genes & Dev 8:1703-1712.
56. Valcárcel J, Gaur RK, Singh R, Green MR. 1996. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273:1706-1709.
57. Valcárcel J, Singh R, Green MR. 1995. Mechanism of regulated pre-mRNA splicing. In: Lamond AI. ed. Pre-mRNA processing. Heidelberg, Germany: Springer-Verlag. pp 97-112.
58. Wang Z, Hoffmann HM, Grabowski PJ. 1995. Intrinsic U2AF binding is modulated by exon enhancer signals in parallel with changes in splicing activity. RNA 1:21-35.
59. Wassarman DA, Steitz JA. 1993. A base-pairing interaction between U2 and U6 small nuclear RNAs occurs in > 150S complexes in HeLa cell extracts: Implications for the spliceosome assembly pathway. Proc Natl Acad Sci USA 90:7139-7143.
60. Wassarman KM, Steitz JA. 1993. Association with terminal exons in pre-mRNAs: A new role for the U1 snRNP? Genes & Dev 7:647-659.
61. Watakabe A, Tanaka K, Shimura Y. 1993. The role of exon sequences in splice site selection. Genes & Dev 7:407-418.
62. Wu Q, Krainer AR. 1996. U1-mediated exon definition interactions between AT-AC and GT-AG introns. Science 274:1005-1008.
63. Wu Q, Krainer AR. 1997. Splicing of a divergent subclass of AT-AC introns requires the major spliceosomal snRNAs. RNA 3:586-601.
64. Yeakley JM, Hedjran F, Morfin JP, Merillat N, Rosenfeld MG, Emeson RB. 1993. Control of calcitonin/calcitonin gene-related peptide pre-mRNA processing by constitutive intron and exon elements. Mol Cell Biol 13:5999-6011.
65. Yeakley JM, Morfin JP, Rosenfeld MG, 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.
66. Yu YT, Steitz JA. 1997. Site-specific crosslinking of mammalian U11 and U6atac to the 5′ splice site of an AT-AC intron. Proc Natl Acad Sci USA 94:6030-6035.
67. Zahler AM, Roth MB. 1995. Distinct functions of SR proteins in recruitment of U1 small nuclear ribonucleoprotein to alternative 5′ splice sites. Proc Natl Acad Sci USA 92:2642-2646.
68. Zuo P, Maniatis T. 1996. The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. Genes & Dev 10:1356-1368.