Enhancer elements activate the weak 3' splice site of α-tropomyosin exon 2

RNA

Volumn 4, Issue 12, 1998, Pages 1523-1536

  Dye, Billy T ^a   Buvoli, Massimo ^b,c,e   Mayer, Stephen A ^b,d   Lin, Chorng Horng ^a   Patton, James G ^a  

^a VANDERBILT UNIVERSITY   (United States)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e Ist Genet Biochim ed E   (Italy)

Author keywords

Exon enhancers; Pre mRNA splicing; SR proteins

Indexed keywords

TROPOMYOSIN;

ALTERNATIVE RNA SPLICING; ARTICLE; COMPETITIVE INHIBITION; COMPLEX FORMATION; ENHANCER REGION; EXON; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION REGULATION; INTRON; MESSENGER RNA SYNTHESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN RNA BINDING; RNA SPLICING;

ALTERNATIVE SPLICING; BASE SEQUENCE; CELLS, CULTURED; ENHANCER ELEMENTS (GENETICS); EXONS; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; RNA, MESSENGER; RNA-BINDING PROTEINS; TROPOMYOSIN;

MAMMALIA;

EID: 0031788402     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838298980360     Document Type: Article

References (62)

1. Abmayr SM, Workman JL, Roeder RG. 1988. The pseudorabies immediate early protein stimulates in vitro transcription by facilitating TFIID:promoter interactions. Genes & Dev 2:542-553.
2. Abovich N, Rosbash M. 1997. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89:403-412.
3. Adams MD, Rudner DZ, Rio DR. 1996. Biochemistry and regulation of pre-mRNA splicing. Curr Opin Cell Biol 8:331-339.
4. Berglund JA, Abovich N, Rosbash M. 1998. A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes & Dev 12:858-867.
5. Berglund JA, Chua K, Abovich N, Reed R, Rosbash M. 1997. The splicing factor BBP interacts specifically with the pre-mRNA branch-point sequence UACUAAC. Cell 89:781-787.
6. Black DL. 1995. Finding splice sites within a wilderness of RNA. RNA 1:763-771.
7. Buvoli M, Mayer SA, Patton JG. 1997. Functional crosstalk between exon enhancers, polypyrimidine tracts, and branch point sequences. EMBO J 16:7174-7183.
8. Chabot B. 1996. Directing alternative splicing: Cast and scenarios. TIG 12:472-478.
9. Coolidge CJ, Seely RJ, Patton JG. 1997. Functional analysis of the polypyrimidine tract in pre-mRNA splicing. Nucleic Acids Res 25:888-896.
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. Dignam JD, Lebovitz RM, Roeder RG. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res 11:1475-1489.
12. Elrick LL, Humphrey MB, Cooper TA, Berget SM. 1998. A short sequence within two purine-rich enhancers determines 5′ splice site specificity. Mol Cell Biol 18:343-352.
13. Englard S, Seifter S. 1990. Precipitation techniques. Methods Enzymol 182:285-300.
14. Fu X-D. 1993. Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365:82-85.
15. Fu X-D. 1995. The superfamily of arginine/serine-rich splicing factors. RNA 1:663-680.
16. Fu X-D, 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.
17. Gooding C, Roberts GC, Moreau G, Nadal-Ginard B, Smith CWJ. 1994. Smooth muscle specific switching of α-tropomyosin mutually exclusive exon selection by specific inhibition of the strong default exon. EMBO J 13:3861-3872.
18. Gooding C, Roberts GC, Smith CWJ. 1998. Role of an inhibitory pyrimidine element and polypyrimidine tract binding protein in repression of a regulated α-tropomyosin exon. RNA 4:85-100.
19. Harlow E, Lane D. 1988. Antibodies. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
20. Hedley ML, Maniatis T. 1991. Sex-specific splicing and polyadenylation of dsx pre-mRNA requires a sequence that binds specifically to tra-2 protein in vitro. Cell 65:579-586.
21. Kohtz JD, Jamison SF, Will CL, Zuo P, Lührmann R, Garcia-Blanco MA, Manley J. 1994. Protein-protein interactions and 5′ splice site recognition in mammalian mRNA precursors. Nature 368:119-124.
22. Laemmli UK. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
23. 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.
24. Lees-Miller JP, Goodwin LO, Helfman DM. 1990. Three novel brain tropomyosin isoforms are expressed from the rat α-tropomyosin gene through the use of alternative promoters and alternative RNA processing. Mol Cell Biol 10:1729-1742.
25. Lin C-H, Patton JG. 1995. Regulation of alternative 3′ splice site selection by constitutive splicing factors. RNA 1:234-245.
26. 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.
27. Manley JL, Tacke R. 1996. SR proteins and splicing control. Genes & Dev 10:1569-1579.
28. Moore MJ, Sharp PA. 1992. Site-specific modification of pre-mRNA: The 2′-hydroxyl groups at the splice sites. Science 256:992-997.
29. Mullen MP, Smith CWJ, Patton JG, Nadal-Ginard B. 1991. α-Tropomyosin mutually exclusive exon selection: Competition between branch point/polypyrimidine tracts determines exon choice. Genes & Dev 5:642-655.
30. Patton JG, Mayer SA, Tempst P, Nadal-Ginard B. 1991. Characterization and molecular cloning of polypyrimidine tract binding protein: A component of a complex necessary for pre-mRNA splicing. Genes & Dev 5:1237-1251.
31. Perez I, Lin C-H, McAfee JG, Patton JG. 1997. Mutation of PTB binding sites causes misregulation of α-tropomyosin alternative 3′ splice site selection in vivo. RNA 3:764-778.
32. Rain J-C, Rafi Z, Rhani Z, Legrain P, Krämer A. 1998. Conservation of functional domains involved in RNA binding and protein-protein interactions in human and Sacchammyces cerevisiae pre-mRNA splicing factor SF1. RNA 4:551-565.
33. Reed R. 1989. The organization of 3′ splice-site sequences in mammalian introns. Genes & Dev 3:2113-2123.
34. Reed R. 1996. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr Opin Gen Dev 6:215-220.
35. Roscigno RF, Weiner M, Garcia-Blanco MA. 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.
36. Rothman A, Kulik TJ, Taubman MB, Berk BC, Smith CWJ, Nadal-Ginard B. 1992. Characterization of a newly established rat pulmonary arterial smooth muscle cell line. Circulation 86:1977-1986.
37. Ryner L, Baker BS. 1991. Regulation of doublesex pre-mRNA processing occurs by 3′ splice site activation. Genes & Dev 5:2071-2085.
38. Screaton GR, Caceres JF, Mayeda A, Bell MV, Plebanski M, Jackson DG, Bell JI, Krainer AR. 1995. Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO J 14:4336-4349.
39. Singh R, Valcarcel J, Green MR. 1995. Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract binding proteins. Science 268:1173-1176.
40. Smith CWJ, 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.
41. Smith CWJ, Patton JG, Nadal-Ginard B. 1989. Alternative splicing in the control of gene expression. Ann Rev Genet 23:527-577.
42. Smith CWJ, Porro EB, Patton JG, Nadal-Ginard B. 1989. Scanning from an independently specified branch point defines the 3′ splice site of mammalian introns. Nature 342:243-247.
43. St Johnston D, Brown NH, Gall JG, Jantsch M. 1992. A conserved double-stranded RNA-binding domain. Proc Natl Acad Sci USA 89:10979-10983.
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. 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.
46. Tanaka K, Watakabe A, Shimura Y. 1994. Polypurine sequences within a downstream exon function as a splicing enhancer. Mol Cell Biol 14:1347-1354.
47. Tian H, Kole R. 1995. Selection of novel exon recognition elements from a pool of random sequences. Mol Cell Biol 15:6291-6298.
48. Tian M, Maniatis T. 1992. Positive control of pre-mRNA splicing in vitro. Science 256:237-240.
49. Tian M, Maniatis T. 1993. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell 74:105-114.
50. Tian M, Maniatis T. 1994. A splicing enhancer exhibits both constitutive and regulated activities. Genes & Dev 8:1703-1712.
51. Valcarcel J, Singh R, Green MR. 1995. Mechanisms of regulated pre-mRNA splicing. In: Lamond AI, ed. Pre-mRNA processing. Austin, Texas: R.G. Landes Company, pp 97-112.
52. Wang J, Manley JL. 1995. Overexpression of the SR proteins ASF/ SF2 and SC35 influences alternative splicing in vivo in diverse ways. RNA 1:335-346.
53. Watakabe A, Tanaka K, Shimura Y. 1993. The role of exon sequences in splice site selection. Genes & Dev 7:407-418.
54. Wieczorek D, Smith CWJ, Nadal-Ginard B. 1988. The rat α-tropomyosin gene generates a minimum of six different mRNAs coding for striated, smooth and non-muscle isoforms by alternative splicing. Mol Cell Biol 8:679-694.
55. Wu JY, Maniatis T. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75:1061-1070.
56. Xiao SH, Manley JL 1997. Phosphorylation of the ASF/SF2 RS domain affects both protein-protein and protein-RNA interactions and is necessary for splicing. Genes & Dev 11:334-344.
57. 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.
58. Yeakley JM, Hedjran F, Morfin J-P, 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.
59. Yeakley JM, Morfin J-P, 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.
60. Zahler AM, Lane WS, Stolk JA, Roth MB. 1992. SR proteins: A conserved family of pre-mRNA splicing factors. Genes & Dev 6:837-847.
61. Zahler AM, Roth M. 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.
62. Zuo P, Manley JL. 1994. The human splicing factor ASF/SF2 can specifically recognize pre-mRNA 5′ splice sites. Proc Natl Acad Sci USA 91:3363-3367.