Genetic analysis of the SR protein ASF/SF2: Interchangeability of RS domains and negative control of splicing

Genes and Development

Volumn 12, Issue 14, 1998, Pages 2222-2233

  Wang, Jin ^a,b   Xiao, Shou Hua ^a   Manley, James L ^a  

^a Columbia University ^*  (United States)

^b ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

Author keywords

Pre mRNA processing; RS domains; Splicing; SR proteins

Indexed keywords

ARGININE; CHIMERIC PROTEIN; MESSENGER RNA PRECURSOR; RNA BINDING PROTEIN; SERINE; VIRUS RNA;

ALTERNATIVE RNA SPLICING; AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; B LYMPHOCYTE; CARBOXY TERMINAL SEQUENCE; CELL GROWTH; CELL VIABILITY; CHICKEN; CONTROLLED STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION;

ANIMALIA; GALLUS GALLUS; HUMAN IMMUNODEFICIENCY VIRUS 1; METAZOA;

EID: 0032527760     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.12.14.2222     Document Type: Article

References (74)

1. Amendt, B.A., Z.H. Si, and C.M. Stoltzfus. 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.
2. Amrein, H., M. Gorman, and R. Nöthiger. 1988. The sex-determining gene tra-2 of Drosophila encodes a putative RNA binding protein. Cell 55: 1025-1035.
3. Amrein, H., M.L. Hedley, and T. Maniatis. 1994. The role of specific protein-RNA and protein-protein interactions in positive and negative control of pre-mRNA splicing by transformer 2. Cell 76: 735-746.
4. Ayane, M., U. Preuss, G. Kohler, and P.J. Nielsen. 1991. A differentially expressed murine RNA encoding a protein with similarities to two types of nucleic acid binding motifs. Nucleic Acids Res. 19: 273-278.
5. Baker, B.S. 1989. Sex in flies: The splice of life. Nature 340: 521-524.
6. Boise, L.H., M. González-Garcia, C.E. Postema, L. Ding, T. Lindsten, L.A. Turka, X. Mao, G. Nuñez, and C.B. Thompson. 1993. bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death. Cell 74: 597-608.
7. Cáceres, J.F. and A.R. Krainer. 1993. Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains. EMBO J. 12: 4715-4726.
8. 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.
9. Cáceres, J.F., T. Misteli, G.R. Screaton, D.L. Spector, and A.R. Krainer. 1997. Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity. J. Cell Biol. 138: 225-238.
10. Cáceres, J.F., G.R. Screaton, and A.R. Krainer. 1998. A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes & Dev. 2: 55-66.
11. Chandler, S.D., A. Mayeda, J.M. Yeakley, A.R. Krainer, and X.D. Fu. 1997. RNA splicing specificity determined by the coordinated action of RNA recognition motifs in SR proteins. Proc. Natl. Acad. Sci. 94: 3596-3601.
12. Dauwalder, B., F. Amaya-Manzanares, and W. Mattox. 1996. A human homologue of the Drosophila sex determination factor transformer-2 has conserved splicing regulatory functions. Proc. Natl. Acad. Sci. 93: 9004-9009.
13. Eperon, I.C., D.C. Ireland, R.A. Smith, A. Mayeda, and A.R. Krainer. 1993. Pathways for selection of 5′ splice sites by U1 snRNPs and SF2/ASF. EMBO J. 12: 3607-3617.
14. Fu, X.D. 1993. Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365: 82-85.
15. _. 1995. The superfamily of arginine/serine-rich splicing factors. RNA 1: 663-680.
16. Fu, X.D. and T. Maniatis. 1990. Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343: 437-441.
17. _. 1992. Isolation of a complementary DNA that encodes the mammalian splicing factor SC35. Science 256: 535-538.
18. Fu, X.D., A. Mayeda, T. Maniatis, and A. Krainer. 1992. General splicing factors SF2 and SC35 have equivalent activities in vitro, and both affect alternative 5′ and 3′ splice site selection. Proc. Natl. Acad. Sci. 89: 11224-11228.
19. 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.
20. Ge, H., P. Zuo, and J.L. Manley. 1991. Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators. Cell 66: 373-382.
21. Goralski, T.J., J.E. Edstrom, and B.S. Baker. 1989. The sex determination locus transformer-2 of Drosophila encodes a polypeptide with similarity to RNA binding proteins. Cell 56: 1011-1018.
22. Harper, J.E. and J.L. Manley. 1992. Multiple activities of the human splicing factor ASF. Gene Expr. 2: 19-29.
23. Hedley, M.L., H. Amrein, and T. Maniatis. 1995. An amino acid sequence motif sufficient for subnuclear localization of an arginine/serine-rich splicing factor. Proc. Natl. Acad. Sci. 92: 11524-11528.
24. Heinrichs, V. and B.S. Baker. 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.
25. Jamison, S.F., Z. Pasman, J. Wang, C. Will, R. Lührmann, J.L. Manley, and M.A. Garcia-Blanco. 1995. U1 snRNP-ASF/SF2 interaction and 5′ splice site recognition: Characterization of required elements. Nucleic Acids Res. 23: 3260-3267.
26. Kanaar, R., S.E. Roche, E.L. Beall, M.R. Green, and D.C. Rio. 1993. The conserved pre-mRNA splicing factor U2AF from Drosophila: Requirement for viability. Science 262: 569-573.
27. Kanopka, A., O. Mühlemann, and G. Akusjärvi. 1996. SR proteins that are essential for generic pre-mRNA splicing inhibit splicing of a regulated adenovirus pre-mRNA. Nature 381: 535-538.
28. Kim, Y.J., P. Zuo, J.L. Manley, and B.S. Baker. 1992. The Drosophila RNA-binding protein RBP1 is localized to transcriptionally active sites of chromosomes and shows a functional similarity to human splicing factor ASF/SF2. Genes & Dev. 6: 2569-2579.
29. 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 368: 119-124.
30. Krainer, A.R., G.C. Conway, and D. Kozak. 1990a. Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes & Dev. 4: 1158-1171.
31. _. 1990b. The essential pre-mRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites. Cell 62: 35-42.
32. Krainer, A.R., A. Mayeda, D. Kozak, and G. Binns. 1991. Functional expression of cloned human splicing factor SF2: Homology to RNA-binding proteins, U170K and Drosophila splicing regulators. Cell 66: 383-394.
33. Krämer, A. 1996. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu. Rev. Biochem. 65: 367-409.
34. a) and tra RNA processing regulators target proteins to a subnuclear compartment implicated in splicing. Cell 67: 335-342.
35. Lynch, K.W. and T. Maniatis. 1995. Synergistic interactions between two distinct elements of a regulated splicing enhancer. Genes & Dev. 9: 284-293.
36. Mackay, A.M., D.M. Eckley, C. Chue, and W.C. Earnshaw. 1993. Molecular analysis of the INCENPs (inner centromere proteins): Separate domains are required for association with microtubules during interphase and with the central spindle during anaphase. J. Cell Biol. 123: 373-385.
37. Manley, J.L. and R. Tacke. 1996. SR proteins and splicing control. Genes & Dev. 10: 1569-1579.
38. Mattox, W. and B.S. Baker. 1991. Autoregulation of the splicing of transcripts from the transformer-2 gene of Drosophila. Genes & Dev. 5: 786-796.
39. McNally, L.M. and M.T. McNally. 1996. SR protein splicing factors interact with the Rous sarcoma virus negative regulator of splicing element. J. Virol. 70: 1163-1172.
40. Misteli, T., J.F. Cáceres, and D.L. Spector. 1997. The dynamics of a pre-mRNA splicing factor in living cells. Nature 387: 523-527.
41. Miyazaki, J., S. Takaki, K. Araki, F. Tashiro, A. Tominaga, K. Takatsu, and K. Yamamura. 1989. Expression vector system based on the chicken beta-actin promoter directs efficient production of interleukin-5. Gene 79: 269-277.
42. Moore, M.J., C.C. Query, and P.A. Sharp. 1993. Splicing of precursors to messenger RNAs by the spliceosome. In The RNA world (ed. R.F. Gesteland and J.F. Atkins), pp. 303-358. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
43. Neugebauer, K.M. and M.B. Roth. 1997. Distribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription. Genes & Dev. 11: 1148-1159.
44. Peng, X. and S.M. Mount. 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.
45. Potashkin, J., K. Naik, and K. Wentz-Hunter. 1993. U2AF homolog required for splicing in vivo. Science 262: 573-575.
46. 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.
47. Ring, H.Z. and J.T. Lis. 1994. The SR protein B52/SRp55 is essential for Drosophila development. Mol. Cell. Biol. 14: 7499-7506.
48. Rudner, D.Z., K.S. Breger, and D.C. Rio. 1998. Molecular genetic analysis of the heterodimeric splicing factor U2AF: The RS domain on either the large or small Drosophila subunit is dispensable in vivo. Genes & Dev. 12: 1010-1021.
49. Screaton, G.R., J.F. Cáceres, A. Mayeda, M.V. Bell, M. Plebanski, D.G. Jackson, J.I. Bell, and A.R. Krainer. 1995. Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO J. 14: 4336-4349.
50. Shi, H., B.E. Hoffman, and J.T. Lis. 1997. A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52. Mol. Cell. Biol. 17: 2649-2657.
51. Staffa, A. and A. Cochrane. 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.
52. 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.
53. 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.
54. Tacke, R. and J.L. Manley. 1995. The human splicing factors ASF/SF2 and SC35 possess different, functionally significant RNA binding specificities. EMBO J. 14: 3540-3551.
55. Tacke, R., Y. Chen, 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. 94: 1148-1153.
56. Tian, M. and T. Maniatis. 1993. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell 74: 105-114.
57. Valcárcel, J. and M.R. Green. 1996. The SR protein family: Pleiotropic functions in pre-mRNA splicing. Trends Biochem. Sci. 21: 296-301.
58. 65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273: 1706-1709.
59. Vellard, M., A. Sureau, J. Soret, C. Martinerie, and B. Perbal. 1992. A potential splicing factor is encoded by the opposite strand of the trans-spliced c-myb exon. Proc. Natl. Acad. Sci. 89: 2511-2515.
60. Wang, J. and J.L. Manley. 1995. Overexpression of the SR proteins ASF/SF2 and SC35 influences alternative splicing in vivo in diverse ways. RNA 1: 335-346.
61. Wang, J., Y. Takagaki, and J.L. Manley. 1996. Targeted disruption of an essential vertebrate gene: ASF/SF2 is essential for cell viability. Genes & Dev. 10: 2588-2599.
62. Wang, Z., H.M. Hoffmann, and P.J. Grabowski. 1995. Intrinsic U2AF binding is modulated by exon enhancer signals in parallel with changes in splicing activity. RNA 1: 21-35.
63. Wu, J.Y. and T. Maniatis. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75: 1061-1070.
64. Xiao, S.H. and J.L. Manley. 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.
65. Zahler, A.M. and M.B. Roth. 1995. Distinct functions of SR proteins in recruitment of U1 small nuclear ribonucleoprotein to alternative 5′ splice sites. Proc. Natl. Acad. Sci. 92: 2642-2646.
66. 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.
67. Zahler, A.M., K.M. Neugenbauer, W.S. Lane, and M.B. Roth. 1993. Distinct functions of SR proteins in alternative pre-mRNA splicing. Science 260: 219-222.
68. Zamore, P.D., J.G. Patton, and M.R. Green. 1992. Cloning and domain structure of the mammalian splicing factor U2AF. Nature 355: 609-614.
69. Zhang, G., K.L. Taneja, R.H. Singer, and M.R. Green. 1994. Localization of pre-mRNA splicing in mammalian nuclei. Nature 372: 809-812.
70. Zhang, M., P.D. Zamore, M. Carmo-Fonesca, A.I. Lamond, and M.R. Green. 1992. Cloning and intracellular localization of the U2 small nuclear ribonucleoprotein auxiliary factor small subunit. Proc. Natl. Acad. Sci. 89: 8769-8773.
71. Zhang, W.J. and J.Y. Wu. 1996. Functional properties of p54, a novel SR protein active in constitutive and alternative splicing. Mol. Cell. Biol. 16: 5400-5408.
72. Zhao, W. and J.L. Manley. 1996. Complex alternative RNA processing generates an unexpected diversity of poly(A) polymerase isoforms. Mol. Cell. Biol. 16: 2378-2386.
73. Zuo, P. and J.L. Manley. 1993. Functional domains of the human splicing factor ASF/SF2. EMBO J. 12: 4727-1737.
74. 35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. Genes & Dev. 10: 1356-1368.