A coactivator of pre-mRNA splicing

Genes and Development

Volumn 12, Issue 7, 1998, Pages 996-1009

  Blencowe, Benjamin J ^a,c   Issner, Robbyn ^a,d   Nickerson, Jeffrey A ^b   Sharp, Phillip A ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF MASSACHUSETTS   (United States)

^c UNIVERSITY OF TORONTO   (Canada)

^d ARIAD PHARMACEUTICALS INC   (United States)

Author keywords

Coactivator; Nuclear matrix; Serine arginine rich splicing factor; Small nuclear ribonucleoprotein particle; Spliceosome

Indexed keywords

ARGININE; MATRIX PROTEIN; MESSENGER RNA PRECURSOR; SERINE;

AMINO ACID SEQUENCE; ARTICLE; CELL NUCLEUS MATRIX; NONHUMAN; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; RNA SPLICING; SPLICEOSOME;

EID: 0032054851     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.12.7.996     Document Type: Article

References (70)

1. Abovich, N. and M. Rosbash. 1997. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89: 403-412.
2. Alzhanova-Ericsson, A.T., X. Sun, N. Visa, E. Kiseleva, T. Wurtz, and B. Daneholt. 1996. A protein of the SR family binds extensively to exonic Balbiani ring pre-mRNA and accompanies the RNA from gene to the nuclear pore. Genes & Dev. 10: 2881-2893.
3. Amrein, H., M.L. Hedley, and T. Maniatis. 1994. The role of specific protein-RNA interactions and protein-protein interactions in positive and negative control of pre-mRNA splicing by transformer 2. Cell 76: 735-746.
4. Barabino, S.M.L., B.J. Blencowe, U. Ryder, B.S. Sproat, and A.I. Lamond. 1990. Targeted snRNP depletion reveals an additional role for mammalian U1 snRNP in spliceosome assembly. Cell 63: 293-302.
5. Berget, S.M. 1995. Exon recognition in vertebrate splicing. J. Biol. Chem. 270: 2411-2414.
6. Black, D. 1995. Finding splice sites within a wilderness of RNA. RNA 1: 763-771.
7. Blencowe, B.J. and S.M.L. Barabino. 1995. Antisense affinity depletion of RNP particles. Methods Mol. Biol. 37: 67-76.
8. Blencowe, B.J., J.A. Nickerson, R. Issner, S. Penman, and P.A. Sharp. 1994. Association of nuclear matrix antigens with exon-containing splicing complexes. J. Cell Biol. 127: 593-607.
9. Blencowe, B.J., R. Issner, J. Kim, P. McCaw, and P.A. Sharp. 1995. New proteins related to the Ser-Arg family of splicing factors. RNA 1: 852-865.
10. Bourquin, J.P., I. Stagljar, P. Meier, P. Moosmann, J. Silke, T. Baechi, O. Georgiev, and W. Schaffner. 1997. A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II. Nucleic Acids Res. 11: 2055-2061.
11. Bregman, D., L. Du, S. van der Zee, and S.L. Warren. 1995. Transcription-dependent redistribution of the large subunit of RNA polymerase II to discrete nuclear domains. J. Cell Biol. 129: 287-298.
12. Brendel, V., P. Bucher, I. Nourbakhsh, B. E. Blaisdell, and S. Karlin. 1992. Methods and algorithms for statistical analysis of protein sequences. Proc. Natl. Acad. Sci. 89: 2002-2006.
13. Cáceres, J.F., T. Mistelli, 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.
14. Carter, K.C., K.L. Taneja, and J.B. Lawrence. 1991. Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus. J. Cell Biol. 115: 1191-1202.
15. Chabot, B. 1996. Directing alternative splicing: Cast and scenarios. Trends Genet. 12: 472-478.
16. Colwill, K., T. Pawson, B. Andrews, J. Prasad, J. Manley, J. Bell, and P. Duncan. 1996. The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J. 15: 265-275.
17. Crispino, J.D., B.J. Blencowe, and P.A. Sharp. 1994. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. Science 265: 1866-1869.
18. Crispino, J.D., J.E. Mermoud, A.I. Lamond, and P.A. Sharp. 1996. Cis-acting elements distinct from the 5′ splice site promote U1-independent pre-mRNA splicing. RNA 2: 664-673.
19. Dignam, J.D., R.M. Lebowitz, and R.G. Roeder. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11: 1475-1489.
20. Fakan, S. and E. Puvion. 1980. The ultrastructural visualization of nuclear and extranucleolar RNA synthesis and distribution. Int. Rev. Cyt. 65: 255.
21. Fay, F., K. Taneja, S. Shenoy, L. Lifshitz, and R. Singer. 1997. Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and poly(A). Exp. Cell Res. 231: 27-37.
22. Fu, X.-D. 1995. The superfamily of arginine/serine-rich splicing factors. RNA 1: 663-680.
23. 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.
24. Gui, J.-F., W.S. Lane, and X.-D. Fu. 1994. A serine kinase regulates intracellular localization of splicing factors in the cell cycle. Nature 369: 678-682.
25. Harlow, E. and D. Lane. 1988. Antibodies: A laboratory manual. Cold Spring Harbor Laboratory. New York, NY.
26. Hedley, M., 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.
27. 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.
28. Huang, S. and D.L. Spector. 1996. Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. J. Cell Biol. 133: 719-732.
29. Huang, S., T. Deerinck, M. Ellisman, and D.L. Spector. 1994. In vivo analysis of the stability and transport of nuclear poly(A)+ RNA. J. Cell Biol. 126: 877-899.
30. Jackson, D.A. and P.R. Cook. 1985. Transcription occurs at the nucleoskeleton. EMBO J. 4: 919-925.
31. Kohtz, J.D., S.F. Jamison, C.L. Will, P. Zuo, R. Luhrmann, 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.
32. Krainer, A.R., G.C. Conway, and D. Kozak. 1990. Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes & Dev. 4: 1158-1171.
33. Krämer, A. 1996. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu. Rev. Biochem. 65: 367-409.
34. Lamond, A.I. and M. Carmo-Fonseca. 1993. The coiled body. Trends Cell Biol. 3: 198-204.
35. Lawrence, J., K. Carter, and X. Xing. 1993. Probing functional organization within the nucleus: Is genome structure integrated with RNA metabolism? Cold Spring Harbor Symp. Quant. Biol 58: 807-818.
36. a) and tra RNA processing regulators target proteins to a subnuclear compartment implicated in splicing. Cell 67: 335-342.
37. Lynch, K. and T. Maniatis. 1996. Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer. Genes & Dev 10: 2089-2101.
38. Manley, J. and R. Tacke. 1996. SR proteins and splicing control. Genes &. Dev. 10: 1569-1579.
39. Mattern, K., R. van Driel, and L. de Jong. 1997. Composition and structure of the nuclear matrix. In Nuclear structure and gene expression (ed. B.R. Curtis), pp. 87-110. Academic Press, New York, NY.
40. Meier, U. and G. Blobel. 1992. Nopp140 shuttles on tracks between nucleus and cytoplasm. Cell 70: 127-138.
41. Mermoud, J., C. Calvio, and A.I. Lamond. 1994. Uncovering the role of Ser/Thr protein phosphorylation in nuclear pre-mRNA splicing. Adv. Prot. Phosphatases 8: 99-118.
42. Misteli, T. and D.L. Spector. 1997. Protein phosphorylation and the nuclear organization of pre-mRNA splicing. Trends Cell Biol. 7: 135-138.
43. 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.
44. Mortillaro, M.J., B.J. Blencowe, X. Wei, H.L. Nakayasu, L. Du, S.L. Warren, P. Sharp, and R. Berezney. 1996. A hyperphosphorylated form of the large subunit of RNA polymerasc II is associated with splicing complexes and the nuclear matrix. Proc. Natl. Acad. Sci. 93: 8253-8257.
45. Nickerson, J.A., G. Krockmalnic, K.M. Wan, C.D. Turner, and S. Penman. 1992. A normally masked nuclear matrix antigen that appears at mitosis on cytoskeleton filaments adjoining chromosomes, centrioles and midbodies. J. Cell Biol. 116: 977-987.
46. Nickerson, J.A., G. Krockmalnic, K.M. Wan, and S. Penman. 1997. The nuclear matrix revealed by eluting chromatin from a cross-linked nucleus. Proc. Natl. Acad. Sci. 94: 4446-4450.
47. Pederson, T. 1998. Thinking about a nuclear matrix, J. Mol. Biol. (in press).
48. Penman, S., B. Blencowe, and J. Nickerson. 1997. The nuclear matrix: Past and present. In Nuclear structure and gene expression, pp. 3-24. Academic Press, New York, NY.
49. Reed, R. 1996. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr. Opin. Genet. Dev. 6: 215-220.
50. Roscigno, R. and M. Garcia-Blanco. 1995. SR proteins escort the U4/U6.U5 tri-snRNP to the spliceosome. RNA 1: 692-706.
51. Roth, M.B., C. Murphy, and J.G. Gall. 1990. A monoclonal antibody that recognizes a phosphorylated epitope stains lamp-brush chromosome loops and small granules in the amphibian germinal vesicle. J. Cell Biol. 111: 2217-2223.
52. Sharp, P.A. 1994. Nobel lecture: Split genes and RNA splicing. Cell 77: 805-815.
53. Smith, H.C., S.G. Harris, M. Zillmann, and S.M. Berget. 1989. Evidence that a nuclear matrix protein participates in pre-mRNA splicing. Exp. Cell Res. 182: 521-533.
54. Spector, D.L. 1993. Macromolecular domains within the cell nucleus. Annu. Rev. Cell Biol. 9: 265-315.
55. Spector, D.L., W.H. Schrier, and H. Busch. 1983. Immunoelectron microscopic localization of snRNPs. Biol Cell 49: 1-10.
56. Spector, D.L., X.-D. Fu, and T. Maniatis. 1991. Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J. 10: 3467-3481.
57. Tian, M. and T. Maniatis. 1992. Positive control of pre-mRNA splicing in vitro. Science 256: 237-240.
58. _. 1993. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell 74: 105-114.
59. Tronchère, H., J. Wang, and X.-D. Fu. 1997. A protein related to splicing factor U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA. Nature 388: 397-400.
60. Valcárcel, J. and M.R. Green. 1996. The SR protein family: Pleiotropic functions in pre-mRNA splicing. Trends Biochem. Sci. 21: 296-301.
61. Verheijen, R., H. Kuijpers, P. Vooijs, W. van Venrooij, and F. Ramaekers. 1986. Distribution of the 70k U1 RNA-associated protein during interphase and mitosis: Correlation with other U RNP particles and proteins of the nuclear matrix. J. Cell Sci. 86: 173-190.
62. Vogelstein, B. and B.F. Hunt. 1982. A subset of small nuclear ribonucleoprotein particle antigens is a component of the nuclear matrix. Biochem. Biophys. Res. Commun. 105: 1224-1232.
63. Wan, K., J.A. Nickerson, G. Krockmalnic, and S. Penman. 1994. The SRm160 protein is in the dense assemblies of the nuclear matrix and relocates to the spindle and pcricentriolar filaments at mitosis. Proc. Natl. Acad. Sci. 91: 594-598.
64. Wansink, D.G., W. Schul, I. van der Kraan, B. van Steensel, R. van Driel, and L. de Jong. 1993. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J. Cell Biol. 122: 283-293.
65. Wu, J.Y. and T. Maniatis. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75: 1061-1070.
66. Xing, Y., C.V. Johnson, P.R. Dobner, and J.B. Lawrence. 1993. Higher level organization of individual gene transcription and splicing. Science 259: 1326-1330.
67. Xing, Y., C. Johnson, P.M. McNeil, Jr., and J. Lawrence. 1995. Nonrandom gene organization: Structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J. Cell Biol. 131: 1635-1647.
68. Zahler, A.M., W.S. Lane, J.A. Stalk, and M.B. Roth. 1992. SR proteins: A conserved family of pre-mRNA splicing factors. Genes & Dev. 6: 837-847.
69. Zeitlin, S., A. Parent, S. Silverstein, and A. Efstratiadis. 1987. Pre-mRNA splicing and the nuclear matrix. Mol. Cell. Biol 7: 111-120.
70. Zeitlin, S., R.C. Wilson, and A. Efstratiadis. 1989. Autonomous splicing and complementation of in vivo assembled spliceosomes. J. Cell Biol. 108: 765-777.