Specific binding of an exonic splicing enhancer by the pre-mRNA splicing factor SRp55

RNA

Volumn 4, Issue 1, 1998, Pages 11-23

  Nagel, Roland J ^a   Lancaster, Alissa M ^a,b   Zahler, Alan M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Alternative splicing; Exonic splicing enhancers; Splicing factors; SR proteins; Troponin T

Indexed keywords

DIMETHYL SULFATE; KETOXAL; MESSENGER RNA PRECURSOR; PROTEIN SUBUNIT; TROPONIN T;

ALTERNATIVE RNA SPLICING; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CHEMICAL MODIFICATION; ENHANCER REGION; EXON; FOWL; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; RNA BINDING; RNA SEQUENCE; RNA SPLICING; RNA STRUCTURE;

ADENOSINE; ALDEHYDES; ANIMALS; BASE SEQUENCE; BIRDS; ENHANCER ELEMENTS (GENETICS); EXONS; GUANOSINE; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION; MYOCARDIUM; NUCLEAR PROTEINS; PHOSPHOPROTEINS; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; SULFURIC ACID ESTERS; TROPONIN; TROPONIN T;

ANIMALIA; AVES; GALLIFORMES;

EID: 0031984931     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (56)

1. Ares M Jr, Weiser B. 1994. Rearrangement of snRNA structure during assembly and function of the spliceosome. Prog Nucleic Acids Res Mol Biol 50:131-159.
2. Berkowitz RD, Luban J, Goff SP. 1993. Specific binding of human immunodeficiency virus type 1 gag polyprotein and nucleocapsid protein to viral RNAs detected by RNA mobility shift assays. J Virol 67:7190-7200.
3. Birney E, Kumar S, Krainer AR. 1993. Analysis of the RNA-recognition motif and RS and RGG domains: Conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res 21:5803-5816.
4. Caceres JF, Stamm S, Helfman DM, Krainer AR. 1994. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science 265:1706-1709.
5. Caputi M, Casari G, Guenzi S, Tagliabue R, Sidoli A, Melo CA, et al. 1994. A novel bipartite splicing enhancer modulates the differential processing of the human fibronectin EDA exon. Nucleic Acids Res 22:1018-1022.
6. Cooper TA, Ordahl CP. 1985. A single cardiac troponin T gene generates embryonic and adult isoforms via developmentally regulated alternate splicing. J Biol Chem 260:11140-11148.
7. Cote GJ, Stolow DT, Peleg S, Berget SM, Gagel RF. 1992. Identification of exon sequences and an exon binding protein involved in alternative RNA splicing of calcitonin/CGRP. Nucleic Acids Res 20:2361-2366.
8. Dreyfuss G, Matunis MJ, Pinol-Roma S, Burd CG. 1993. hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 62:289-321.
9. Fu XD. 1993. Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365:82-85.
10. Fu XD. 1995. The superfamily of arginine/serine-rich splicing factors. RNA 1:663-680.
11. Fu XD, Maniatis T. 1992. The 35-kDa mammalian splicing factor SC35 mediates specific interactions between U1 and U2 small nuclear ribonucleoprotein particles at the 3′ splice site. Proc Natl Acad Sci USA 89:1725-1729.
12. Ge H, Manley JL. 1990. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell 62:25-34.
13. 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.
14. Heinrichs V, Baker BS. 1995. The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences. EMBO J 14:3987-4000.
15. Jamison SF, Pasman Z, Wang J, Will C, Luhrmann R, Manley JL, et al. 1995. U1 snRNP-ASF/SF2 interaction and 5′ splice site recognition: Characterization of required elements. Nucleic Acids Res 23:3260-3267.
16. Kanopka A, Muhlemann O, Akusjarvi G. 1996. Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA. Nature 381:535-538.
17. Kenan DJ, Query CC, Keene JD. 1991. RNA recognition: Towards identifying determinants of specificity. Trends Biochem Sci 16:214-220.
18. Kim YJ, Zuo P, Manley JL, Baker BS. 1992. The Drosophila RNA-binding protein RBP1 is localized to transcriptionally active sites of chromosomes and shows functional similarity to human splicing factor ASF/SF2. Genes & Dev 6:2569-2579.
19. Kohtz JD, Jamison SF, Will CL, Zuo P, Luhrmann R, Garcia-Blanco MA, et al. 1994. Protein-protein interactions and 5′ splice-site recognition in mammalian mRNA precursors. Nature 368:119-124.
20. Krainer AR, Conway GC, Kozak D. 1990. Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes & Dev 4:1158-1171.
21. 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 7:2405-1417.
22. Libri D, Goux PM, Brody E, Fiszman MY. 1990. Exon as well as intron sequences are cis-regulating elements for the mutually exclusive alternative splicing of the beta tropomyosin gene. Mol Cell Biol 10:5036-5046.
23. Lynch KW, Maniatis T. 1996. Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila double-sex splicing enhancer. Genes & Dev 10:2089-2101.
24. Manley JL, Tacke R. 1996. SR proteins and splicing control. Genes Dev 10:1569-1579.
25. Mardon HJ, Sebastio G, Barralle FE. 1987. A role for exon sequences in alternative splicing of the human fibronectin gene. Nucleic Acids Res 15:7725-7733.
26. Mayeda A, Zahler AM, Krainer AR, Roth MB. 1992. Two members of a conserved family of nuclear phosphoproteins are involved in general and alternative pre-mRNA splicing. Proc Natl Acad Sci USA 89:1301-1304.
27. Moazed D, Stern S, Noller HF. 1986. Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. J Mol Biol 187:399-416.
28. Moore MJ, Query CC, Sharp PA. 1993. Splicing of precursors to mRNA by the spliceosome. In: Gesteland RF, Atkins JF, eds. The RNA world. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. pp 303-357.
29. Nilsen TW. 1994. RNA-RNA interactions in the spliceosome: Unraveling the ties that bind. Cell 78:1-4.
30. Peng X, Mount SM. 1995. Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor. Mol Cell Biol 15:6273-6282.
31. 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.
32. Roscigno RF, Garcia-Blanco MA. 1995. SR proteins escort the U4/ U6.U5 tri-snRNP to the spliceosome. RNA 1:692-706.
33. Ruskin B, Krainer AR, Maniatis T, Green MR. 1984. Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell 38:317-331.
34. Sharp PA. 1994. Split genes and RNA splicing. Cell 77:805-815.
35. Shi H, Hoffman BE, Lis JT. 1997. A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52. Mol Cell Biol 17:2649-2657.
36. Staknis D, Reed R. 1994. SR proteins promote the first specific recognition of the 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.
37. Stern S, Moazed D, Noller HF. 1988. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol 164:481-489.
38. Streuli M, Saito H. 1989. Regulation of tissue-specific alternative splicing: Exon-specific cis-elements govern the splicing of leukocyte common antigen pre-mRNA. EMBO J 8:787-796.
39. Sun Q, Hampson RK, Rottman FM. 1993a. In vitro analysis of bovine growth hormone pre-messenger RNA alternative splicing-Involvement of exon sequences and trans-acting factor(s). J Biol Chem 268:15659-15666.
40. Sun Q, Mayeda A, Hampson RK, Krainer AR, Rottman FM. 1993b. General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes & Dev 7:2598-2608.
41. Tacke R, Chen Y, Manley JL. 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.
42. 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.
43. Tanaka K, Watakabe A, Shimura Y. 1994. Polypurine sequences within a downstream exon function as a splicing enhancer. Mol Cell Biol 14:1347-1354.
44. Tian M, Maniatis T. 1993. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell 74:105-114.
45. Tsai AY, Streuli M, Saito H. 1989. Integrity of the exon 6 sequence is essential for tissue-specific alternative splicing of human leukocyte common antigen pre-mRNA. Mol Cell Biol 9:4550-4555.
46. van Oers CM, Adema GJ, Zandberg H, Moen TC, Baas PD. 1994. Two different sequence elements within exon 4 are necessary for calcitonin-specific splicing of human calcitonin/calcitonin gene-related peptide 1 pre-mRNA. Mol Cell Biol 14:951-960.
47. Wakamatsu N, Kobayashi H, Miyatake T, Tsuji S. 1992. A novel exon mutation in the human beta-hexosaminidase beta subunit gene affects 3′ splice site selection. J Biol Chem 267:2406-2413.
48. Wang J, Takagaki Y, Manley JL. 1996. Targeted disruption of an essential vertebrate gene: ASF/SF2 is required for cell viability. Genes & Dev 10:2588-2599.
49. Watakabe A, Sakamoto H, Shimura Y. 1991. Repositioning of an alternative exon sequence of mouse IgM pre-mRNA activates splicing of the preceding intron. Gene Expression 1:175-184.
50. Watakabe A, Tanaka K, Shimura Y. 1993. The role of exon sequences in splice site selection. Genes & Dev 7:407-418.
51. Wilson C, Szostak JW. 1995. In vitro evolution of a self-alkylating ribozyme. Nature 374:777-782.
52. Wu JY, Maniatis T. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75:1061-1070.
53. Xu R, Teng J, Cooper TA. 1993. The cardiac troponin T alternative exon contains a novel purine-rich positive splicing element. Mol Cell Biol 13:3660-3674.
54. Zahler AM, Lane WS, Stolk JA, Roth MB. 1992. SR proteins: A conserved family of pre-mRNA splicing factors. Genes & Dev 6:837-847.
55. Zahler AM, Neugebauer KM, Lane WS, Roth MB. 1993. Distinct functions of SR proteins in alternative pre-mRNA splicing. Science 260:219-222.
56. 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.