SR-related proteins and the processing of messenger RNA precursors

Biochemistry and Cell Biology

Volumn 77, Issue 4, 1999, Pages 277-291

  Blencowe, Benjamin J ^a   Bowman, John A L ^a   McCracken, Susan ^a   Rosonina, Emanuel ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Nuclear matrix; Polyadenylation; RNA polymerase; Spliceosome; SR protein

Indexed keywords

RNA PRECURSOR;

AMINO ACID SEQUENCE; CONFERENCE PAPER; MESSENGER RNA SYNTHESIS; NONHUMAN; POLYADENYLATION; PROTEIN PROCESSING; SPLICEOSOME;

METAZOA;

EID: 0032710804     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o99-048     Document Type: Conference Paper

References (157)

1. Abovich, N., and Rosbash, M. 1997. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell, 89: 403-412.
2. Abovich, N., Liao, X.C., and Rosbash, M. 1994. The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes Dev. 8: 843-854.
3. Allison, L.A., Moyle, M., Shales, M., and Ingles, C. J. 1985. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell, 42: 599-610.
4. Alzhanova-Ericsson, A.T., Sun, X., Visa, N., Kiseleva, E., Wurtz, T., and Daneholt, B. 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.
5. Ayane, M., Preuss, U., Köhler, G., and Nielsen, P J. 1991. A differentially expressed murine RNA encoding a protein with similarities to two types of nucleic acid binding motifs. Nucleic Acids Res. 19: 1273-1278.
6. Bauren, G., and Wieslander, L. 1994. Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell, 76: 183-192.
7. Beil, B., Screaton, G., and Stamm, S. 1997. Molecular cloning of htra2-beta-l and htra2-beta-2, two human homologs of tra-2 generated by alternative splicing. DNA Cell Biol. 16: 679-960.
8. Beyer, A.L., and Osheim, Y.N. 1988. Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev. 2: 754-765.
9. Blencowe, B.J., and Ouzounis, C.A. 1999. The PWI motif: a new protein domain in splicing factors. Trends Biochem. Sci. 24: 179-180.
10. Blencowe, B.J., Nickerson, J.A., Issner, R., Penman, S., and Sharp, P. A. 1994. Association of nuclear matrix antigens with exon-containing splicing complexes. J. Cell Biol. 127: 593-607.
11. Blencowe, B.J., Issner, R., Kim, J., McCaw, P., and Sharp, P.A. 1995. New proteins related to the Ser-Arg family of splicing factors. RNA, 1: 852-865.
12. Blencowe, B.J., Issner, R., Nickerson, J.A., and Sharp, P.A. 1998. A coactivalor of pre-mRNA splicing. Genes Dev. 12: 996-1009.
13. Bourquin, J. P., Stagljar, I., Meier, P., Moosmann, P., Silke, J., Baechi, T., Georgiev, O., and Schaffner, W. 1997. A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II. Nucleic Acids Res. 11: 2055-2061.
14. Burge, C., Tuschl, T., and Sharp, P.A. 1999. RNA World II. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
15. Caceres, J.F., Screaton, G.R., and Krainer, A.R. 1998. A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes Dev. 12: 55-66.
16. Carmo-Fonseca, M., Pepperkok, R., Carvalho, M.T., and Lamond, A. I. 1992. Transcription-dependent colocalization of the U1, U2, U4/U6, and U5 snRNPs in coiled bodies. J. Cell Biol. 117: 1-14.
17. Cavaloc, Y., Popielarz, M., Fuchs, J.-P., Gattoni, R., and Stévenin, J. 1994. Characterization and cloning of the human splicing factor 9G8: a novel 35 kDa factor of the serine/arginine family. EMBO J. 13: 2639-2649.
18. Champlin, D.T., Frasch, M., Saumweber, H., and Lis, J.T. 1991. Characterization of a Drosophilu protein associated with boundaries of transcriptionally active chromatin. Genes Dev. 5: 1611-1621.
19. Chang, D.D., and Sharp, P. A. 1989. Regulation by HIV Rev depends upon recognition of splice sites. Cell, 59: 789-795.
20. Cho, E.J., Takagi, T., Moore, C.R., and Buratowski, S. 1997. mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. II: 3319-3326.
21. Colgan, D.F., and Manley, J.L. 1997. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11: 2755-2766.
22. Colwill, K., Pawson, T., Andrews, B., Prasad, J., Manley, J., Bell, J., and Duncan, P. 1996. The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J. 15: 265-275.
23. Company, M., Arenas, J., and Abelson, J. 1991. Requirement of the RNA helicase-like protein PRP22 for release of messenger RNA from spliceosomes. Nature (London), 349: 487-493.
24. Corden, J.L. 1990. Tails of RNA polymerase II. Trends Biochem. Sci. 15: 383-387.
25. Corden, J.L., and Patturajan, M. 1997. A CTD function linking transcription to splicing. Trends Biochem. Sci. 22: 413-416.
26. Corden, J.L., Cadena, D.L., Ahearn, Jr., J.M., and Dahmus, M.E. 1985. A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A. 82: 7934-7938.
27. Cramer, P., Pesce, C.G., Baralle, F.E., and Kornblihtt, A.R. 1997. Functional association between promoter structure and transcript alternative splicing. Proc. Natl. Acad. Sci. U.S.A. 94: 11 456 -11 460.
28. Crispino, J.D., Blencowe, B.J., and Sharp, P.A. 1994. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. Science (Washington, D.C.). 265: 1866-1869.
29. Custodio, N., Carmo-Fonseca, M., Geraghty, F., Pereira, H.S., Grosveld, F., and Antoniou, M. 1999. Inefficient processing impairs release of RNA from the site of transcription. EMBO J. 18: 2855-2866.
30. Dahmus, M.E. 1996. Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271: 19009 - 19012.
31. Dalbadie-McFarland, G., and Abelson, J. 1990. PRP5: A helicase-like protein required for mRNA splicing in yeast. Proc. Natl. Acad. Sci. U.S.A. 87: 4236-4240.
32. Dauwalder, B., Amaya-Manzanares, F., and Mattox, W. 1996. A human homologue of the Drosophila sex determination factor transformer-2 has conserved splicing regulatory functions. Proc. Natl. Acad. Sci. U.S.A. 93: 9004-9009.
33. de la Cruz. J., Kressler, D., and Linder, P. 1999. Unwinding RNA in: DEAD-box proteins and related families. Trends Biochem. Sci. 24: 192-198.
34. Denhez, F., and Lafyatis, R. 1994. Conservation of regulated alternative splicing and identification of functional domains in vertebrate homologs to the Drosophila regulator, suppressor-of-white-apricot. J. Biol. Chem. 269: 16 170 - 16 179.
35. Diamond, R.H., Du, K., Lee, V.M., Mohn, K.L., Haber, B.A., Tewari, D.S., and Taub, R. 1993. Novel delayed-early and highly insulin-induced growth response genes. J. Biol. Chem. 268: 15 185 - 15 192.
36. Du, L., and Warren, S. 1997. A functional interaction between the carboxy-terminal domain of RNA polymerase II and pre-mRNA splicing. J. Cell Biol. 136: 5-18.
37. Duncan, P.I., Stojdl, D.F., Marius, R.M., Scheit, K.H., and Bell, J. C. 1998. The Clk2 and Clk3 dual-specificity protein kinases regulate the intranuclear distribution of SR proteins and influence pre-mRNA splicing. Exp. Cell Res. 241: 300-308.
38. Eldridge, A.G., Li, Y., Sharp, P.A., and Blencowe, B.J. 1999. The SRm 160/300 splicing coactivator is required for exon-enhancer function. Proc. Natl. Acad. Sci. U.S.A. 96: 6125-6130.
39. Fetzer, S., Lauber, J., Will, C.L., and Luhrmann, R. 1997. The [U4/U6.U5] tri-snRNP-specific 27K protein is a novel SR protein. RNA, 3: 344-355.
40. Fu, X.-D. 1993. Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature (London), 365: 82-85.
41. Fu, X.-D. 1995. The superfamily of arginine/serine-rich splicing factors. RNA. 1: 663-680.
42. Fu, X.-D., and 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. U.S.A. 89: 1725-1729.
43. Fu, X.-D., Mayeda, A., Maniatis, T., and Krainer, A.R. 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. U.S.A. 89: 11 224 - 11 228.
44. Ge, H., and Manley, J.L. 1990. A protein factor, ASF, controls cell specific alternative splicing of SV40 early pre-mRNA in vitro. Cell, 62: 25-34.
45. Ge, H., Zuo, P., and Manley, J. 1991. Primary structure of the human splicing factor ASF reveals similarities with Drosphila regulators. Cell, 66: 373-382.
46. Ge, H., Si, Y., and Wolffe, A.P. 1998. A novel transcriptional coactivator, p52, functionally interacts with the essential splicing factor ASF/SF2. Mol. Cell, 2: 751-759.
47. Greenleaf, A.L. 1993. Positive patches and negative noodles: linking RNA processing to transcription? Trends Biochem. Sci. 18: 117-119.
48. Gross, T., Richert, K., Mierke, C., Lutzelberger, M., and Kaufer, N. F. 1998. Identification and characterization of srp1, a gene of fission yeast encoding a RNA binding domain and a RS domain typical of SR splicing factors. Nucleic Acids Res. 26: 505-511.
49. Gui, J.-F., Lane, W.S., and Fu, X.-D. 1994. A serine kinase regulates intracellular localization of splicing factors in the cell cycle. Nature (London), 369: 678-682.
50. Gunderson, S.I., Beyer, K., Martin, G., Keller, W., Boelens, W.C., and Mattaj, L. W. 1994. The human U1A snRNP protein regulates polyadenylation via a direct interaction with poly(A) polymerase. Cell, 76:531-541.
51. Gunderson, S.I., Polycarpou-Schwarz, M., and Mattaj, I.W. 1998. U1 snRNP inhibits pre-mRNA polyadenylation through a direct interaction between U1 70K and poly(A) polymerase. Mol. Cell, 1: 255-264.
52. Hanes, J., von der Kammer, H., Klaudiny, J., and Scheit, K.H. 1994. Characterization by cDNA cloning of two new human protein kinases. Evidence by sequence comparison of a new family of mammalian protein kinases. J. Mol. Biol. 244: 665-672.
53. Medley, M., Amrein, H., and Maniatis, T. 1995. An amino acid sequence motif sufficient for subnuclear localization of an arginine/serine-rich splicing factor. Proc. Natl. Acad. Sci. U.S.A. 92: 11524-11528.
54. Hirose, Y., Tacke, R., and Manley, J.L. 1999. Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13: 1234-1239.
55. Inoue, K., Hoshijima, K., Higuchi, I., Sakamoto, H., and Shimura, Y. 1992. Binding of the Drusophila transformer and transformer-2 proteins to the regulatory elements of doublesex primary transcript for sex-specific RNA processing. Proc. Natl. Acad. Sci. U.S.A. 89: 8092-8096.
56. Johnson, K.W., and Smith, K.A. 1991. Molecular cloning of a novel human cdc2/CDC28-like protein kinase. J. Biol. Chem. 266: 3402-3407.
57. Kan, J.L.C., and Green, M.R. 1999. Pre-mRNA splicing of IgM exons M1 and M2 is directed by a juxtaposed splicing enhancer and inhibitor. Genes Dev. 13: 462-471.
58. Kanopka, A., Muhlemann, O., Petersen-Mahrt, S., Estmer, C., Ohrmalm, C., and Akusjarvi, G. 1998. Regulation of adenovirus alternative RNA splicing by dephosphorylation of SR proteins. Nature (London), 393: 185-187.
59. Kim, Y.J., Zuo, P., Manley, J.L., and Baker, B.S. 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.
60. Kim, E., Du, L., Bregman, D., and Warren, S. 1997. Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNA. J. Cell Biol. 136: 19-28.
61. Kohtz, J.D., Jamison, S.F., Will, C.L., Zuo, P., Lührmann, R., Garcia-Blanco, M. A., and Manley, J.L. 1994. Protein-protein interactions and 5′-splice-site recognition in mammalian mRNA precursors. Nature (London), 368: 119-124.
62. Koleske, A.J., and Young, R.A. 1995. The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem. Sci. 20: 113-116.
63. Krainer, A.R., Conway, G.G., and Kozak, D. 1990. The essential pre-mRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites. Cell, 62: 35-42.
64. Krainer, A.R., Mayeda, A., Kozak, D., and Binns, G. 1991. Functional expression of cloned human splicing factor SF2: homology to RNA binding proteins, U1 70K, and Drosophila splicing regulators. Cell. 66: 383-394.
65. Kramer, A. 1996. The structure and function of proteins involved in mammalian pre-mRNA splicing. Ann. Rev. Biochem. 65: 367-409.
66. Lai, M.C., Teh, B.H., and Tarn, W.Y. 1999. A human papillomavirus E2 transcriptional activator. The interactions with cellular splicing factors and potential function in pre-mRNA processing. J Biol. Chem. 274: 11 832 - 11 841.
67. Lawrence, J., Carter, K., and Xing, X. 1993. Probing functional organization within the nucleus: is genome structure integrated with RNA metabolism? Cold Spring Harbor Symp. Quant. Biol. 58: 807-818.
68. Lazar, G., Schaal, T., Maniatis, T., and Goodman, H.M. 1995. Identification of a plant serine-arginine-rich protein similar to the mammalian splicing factor SF2/ASF. Proc. Natl. Acad. Sci. U.S.A. 92: 7672-7676.
69. Lee, M.S., Henry, M., and Silver, P.A. 1996. A protein that shuttles between the nucleus and the cytoplasm is an important mediator of RNA export. Genes Dev. 10: 1233-1246.
70. Legrain, P., and Rosbash, M. 1989. Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm. Cell, 57: 573-583.
71. a) and tra RNA processing regulators target proteins to a subnuclear compartment implicated in splicing. Cell, 67: 335-342.
72. Li, Y., and Blencowe, B.J. 1999. Distinct factor requirements for exonic splicing enhancer function and binding of the U2 snRNP auxiliary factor to the polypyrimidine tract. J. Biol. Chem. In press.
73. Lopato, S., Waigmann, E., and Barta, A. 1996. Characterization of a novel arginine/serine-rich splicing factor in Arabidopsis. Plant Cell, 8: 2255-2264.
74. Lopez, A.J. 1998. Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu. Rev. Genet. 32: 279-305.
75. Lou, H., Yang, Y., Cote, G.J., Berget, S.M., and Gagel, R.F. 1995. An intron enhancer containing a 5′ splice site sequence in the human calcitonin/calcitonin gene-related peptide gene. Mol. Cell Biol. 15: 7135-7142.
76. Lou, H., Gagel, R.F., and Berget, S.M. 1996. An intron enhancer recognized by splicing factors activates polyadenylation. Genes Dev. 10: 208-219.
77. Lou, H., Neugebauer, K.M., Gagel, R.F., and Berget, S.M. 1998. Regulation of alternative polyadenylation by U1 snRNPs and SRp20. Mol. Cell Biol. 18: 4977-4985.
78. Lutz, C. S., and Alwine, J.C. 1994. Direct interaction of the U1 snRNP-A protein with the upstream efficiency element of the SV40 late polyadenylation signal. Genes Dev. 8: 576-586.
79. Lutz, C.S., Murthy, K.G., Schek, N., O'Connor, J.P., Manley, J.L., and Alwine, J. C. 1996. Interaction between the U1 snRNP A protein and the 160-kD subunit of cleavage-polyadenylation specificity factor increases polyadenylation efficiency in vitro. Genes Dev. 10: 325-337.
80. Lynch, K.W., and Maniatis, T. 1995. Synergistic interactions between two distinct elements of a regulated splicing enhancer. Genes Dev. 9: 284-293.
81. Lynch, K., and Maniatis, T. 1996. Assembly of specific SR protein complexes on distinct regulatory elements of the Drosphila doublesex splicing enhancer. Genes Dev. 10: 2089-2101.
82. Manley, J., and Tacke, R. 1996. SR proteins and splicing control. Genes Dev. 10: 1569-1579.
83. Mayeda, A., and Krainer, A.R. 1992. Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell, 69: 365-375.
84. Mayeda, A., Munroe, S.H., Caceres, J.F., and Krainer, A.R. 1994. Function of conserved domains of hnRNP A1 and other hnRNP A/B proteins. EMBO J. 13: 5483-5495.
85. McCracken, S., Fong, N., Rosonina, E., Yankulov, K., Brothers, G., Siderovski, D., Hessel, A., Foster, S., Shuman, S., and Bentley, D. L. 1997a. 5′-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 11: 3306-3318.
86. McCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S., Wickens, M., and Bentley, D. L. 1997b. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature (London), 385: 357-361.
87. Mermoud, J.H., Cohen, P.T., and Lamond, A.I. 1994. Regulation of mammalian spliceosome assembly by a protein phosphorylation mechanism. EMBO J. 13: 5679-5688.
88. Misteli, T. 1999. RNA splicing: What has phosphorylation got to do with it? Curr. Biol. 9: 198-200.
89. Misteli, T., Caceres, J.F., and Specter, D.L. 1997. The dynamics of a pre-mRNA splicing factor in living cells. Nature (London), 387: 523-527.
90. Mortillaro, M.J., Blencowe, B.J., Wei, X., Nakayasu, H., Du, L., Warren, S.L., Sharp, P.A., and Berezney, R. 1996. A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix. Proc. Natl. Acad. Sci. U.S.A. 93: 8253-8257.
91. Murray, M.V., Kobayashi, R., and Krainer, A.R. 1999. The type 2C Ser/Thr phosphatase PP2Cgamma is a pre-mRNA splicing factor. Genes Dev. 13: 87-97.
92. O'Keefe, R.T., Mayeda, A., Sadowski, C.L., Krainer, A.R., and Spector, D. L. 1994. Disruption of pre-mRNA splicing in vivo results in reorganization of. J. Cell Biol. 124: 249-260.
93. Ohno, M., and Shimura, Y. 1996. A human RNA helicase-like protein. HRH1, facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. Genes Dev. 10: 997-1007.
94. Ono, Y., Ohno, M., and Shimura, Y. 1994. Identification of a putative RNA helicase (HRH1), a human homolog of yeast Prp22. Mol. Cell. Biol. 14: 7611-7620.
95. Ortlepp, D., Laggerbauer, B., Mullner, S., Achsel, T., Kirschbaum, B., and Luhrmann, R. 1998. The mammalian homologue of Prp16p is overexpressed in a cell line tolerant to Leflunomide, a new immunoregulatory drug effective against rheumatoid arthritis. RNA, 4: 1007-1018.
96. Parvin, J.D., and Young, R.A. 1998. Regulatory targets in the RNA polymerase II holoenzyme. Curr. Opin. Genet. Dev. 8: 565-570.
97. Patturajan, M., Wei, X., Berezney, R., and Corden, J. L. 1998. A nuclear matrix protein interacts with the phosphorylated C-terminal domain of RNA polymerase II. Mol. Cell Biol. 18: 2406-2415.
98. Penman, S., Blencowe, B., and Nickerson, J. 1997. The nuclear matrix: past and present. In Nuclear structure and gene expression. Edited by R.C. Bird. Academic Press, New York. pp. 3-24.
99. Potashkin, J., Naik, K., and Wentz-Hunter, K. 1993. U2AF homolog required for splicing in vivo. Science (Washington, D.C.), 262: 573-575.
100. Puigserver, P., Wu, Z., Park, C. W., Graves, R., Wright, M., and Spiegelman, B.M. 1998. A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis. Cell, 92: 829-839.
101. Query. C.C., Bentley, R.C., and Keene, J.D. 1989. A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein. Cell, 57: 89-101.
102. Reed, R., and Palandjian, L. 1997. Spliceosome assembly. In Eukaryotic mRNA processing. Edited by A.R. Krainer. IRL Press, Oxford.
103. Roscigno, R., and Garcia-Blanco, M. 1995. SR proteins escort the U4/U6.U5 tri-snRNP to the spliceosome. RNA, 1: 692-706.
104. Roth, M. B., Murphy, C., and Gall, J.G. 1990. A monoclonal anti-body that recognizes a phosphorylated epitope stains lampbrush chromosome loops and small granules in the amphibian germinal vesicle. J. Cell. Biol. 111: 2217-2223.
105. Rudner, D.Z., Breger, K.S., and Rio, D.C. 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.
106. Ruegsegger, U., Blank, D., and Keller, W. 1998. Human pre-mRNA cleavage factor Im is related to spliceosomal SR proteins and can be reconstituted in vitro from recombinant subunits. Mol. Cell, 1: 243-253.
107. Ruskin, B., Zamore, P.D., and Green, M.R. 1988. A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly. Cell, 52: 207-219.
108. Schwer, B., and Guthrie, C. 1991. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature (London), 349: 494-499.
109. Schwer, B., and Guthrie, C. 1992. A conformational rearrangement in the spliceosome is dependent on PRP16 and ATP hydrolysis. EMBO J. 11: 5033-5039.
110. Screaton, G.R., Caceres, J.F., Mayeda, A., Bell, M.V., Plebanski, M., Jackson, D.G., Bell, J. I., and Krainer, A.R. 1995. Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO J. 14: 4336-4349.
111. Smith, V., and Barrell, B.C. 1991. Cloning of a yeast U1 snRNP 70K protein homologue: functional conservation of an RNA-binding domain between humans and yeast. EMBO J. 10: 2627-2634.
112. Soret, J., Gattoni, R., Guyon, C., Sureau, A., Popielarz, M., Le Rouzic, E., Dumon, S., Apiou, F., Dutrillaux, B., Voss, H., Ansorge, W., Stevenin, J., and Perbal, B. 1998. Characterization of SRp46, a novel human SR splicing factor encoded by a PR264/SC35 retropseudogene. Mol. Cell Biol. 18: 4924-4934.
113. Specter, D. 1993. Macromolecular domains within the cell nucleus. Ann. Rev. Cell Biol. 9: 265-315.
114. Spikes, D.A., Kramer, J., Bingham, P.M., and Van Doren, K. 1994. SWAP pre-mRNA splicing regulators are a novel, ancient protein family sharing a highly conserved sequence motif with the prp21 family of constitutive splicing proteins. Nucleic Acids Res. 22: 4510-4519.
115. Spritz, R.A., Strunk, K., Surowy, C.S., Hoch, S.O., Barton, D.E., and Francke, U. 1987. The human U1-70K snRNP protein: cDNA cloning, chromosomal localization, expression, alternative splicing and RNA-binding. Nucleic Acids Res. 15: 10 373 -10 391.
116. Staknis, D., and Reed, R. 1994. SR proteins promote the first specific recognition of Pre-mRNA and are present together with the U1 small nuclear ribonucleoprotein particle. Mol. Cell Biol. 14: 7670-7682.
117. Staley, J.P., and Guthrie, C. 1998. Mechanical devices or the spliceosome: motors, clocks, springs, and things. Cell, 92: 315-326.
118. Staley, J.P., and Guthrie, C. 1999. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell, 3: 55-64
119. Steinmetz, E.J. 1997. Pre-mRNA processing and the CTD of RNA polymerase II: the tail that wags the dog? Cell, 89: 491-494.
120. Steinmetz, E. J., and Brow, D. A. 1998. Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association. Proc. Natl. Acad. Sci. U.S.A. 95: 6699-6704.
121. Sukegawa, J., and Blobel, G. 1995. A putative mammalian helicase with an arginine-serine-rich domain colocalizes with a splicing factor. J. Biol. Chem. 270: 15 702 - 15 706.
122. Tacke, R., Tohyama, M., Ogawa, S., and Manley, J.L. 1998. Human Tra2 proteins are sequence-specific activators of pre-mRNA splicing. Cell, 93: 139-148.
123. Takagaki, Y., Seipelt, R.L., Peterson, M.L., and Manley, J.L. 1996. The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation. Cell, 87: 941-952.
124. Tanner, S., Stagljar, L, Georgiev, O., Schaffner, W., and Bourquin, J. P. 1997. A novel SR-related protein specifically interacts with the carboxy- terminal domain (CTD) of RNA polymerase II through a conserved interaction domain. Biol. Chem. 378: 565-571.
125. Tarn, W.-Y., and Steitz, J.A. 1994. SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes Dev. 8: 2704-2717.
126. Tazi, J., Kornstadt, U., Rossi, F., Jeanteur, P., Cathala, G., Brunel, C., and Luhrmann, R. 1993. Thiophosphorylation of U1-70K protein inhibits pre-mRNA splicing. Nature (London), 363: 283-286.
127. Teigelkamp, S., Mundt, C., Achsel, T., Will, C.L., and Luhrmann, R. 1997. The human U5 snRNP-specific 100-kD protein is an RS domain-containing, putative RNA helicase with significant homology to the yeast splicing factor Prp28p. RNA, 3: 1313-1326.
128. Theissen, H., Etzerodt, M., Reuter, R., Schneider, C., Lottspeich, F., Argos, P., Luhrmann, R., and Philipson, L. 1986. Cloning of the human cDNA for the U1 RNA-associated 70K protein. EMBO J. 5: 3209-3217.
129. Tian, M., and Maniatis, T. 1993. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell, 74: 105-114.
130. Tian, M., and Maniatis, T. 1994. A splicing enhancer exhibits both constitutive and regulated activities. Genes Dev. 8: 1703-1712.
131. Tronchere, H., Wang, J., and Fu, X.-D. 1997. A protein related to splicing factor U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA. Nature (London), 388: 397-400.
132. Valcarcel, J., and Green, M.R. 1996. The SR protein family: pleiotropic functions in pre-mRNA splicing. Trends Biochem. Sci. 21: 296-301.
133. Valcárcel, J., Zamore, P.D., Singh, R., and Green, M.R. 1993. The protein Sex-lethal antagonizes the splicing factor U2AF to regulate tra alternative splicing of transformer pre-mRNA. Nature (London), 362: 171-175.
134. Vellard, M., Sureau, A., Soret, J., Martinerie, C., and Perbal, B. 1992. A potential splicing factor is encoded by the opposite strand or the trans-spliced c-myb exon. Proc. Natl. Acad. Sci. U.S.A. 89: 2511-2515.
135. Vincent, M., Lauriault, P., Dubois, M., Lavoie, S., Bensaude, O., and Chabot, B. 1996. The nuclear matrix protein p255 is a highly phosphorylated form or RNA polymerase II largest subunit which associates with spliceosomes. Nucleic Acids Res. 24: 4649-4652.
136. Visa, N., Alzhanova-Ericsson, A.T., Sun, X., Kiseleva, E., Bjorkroth, B., Wurtz, T., and Daneholt, B. 1996. A pre-mRNA-binding protein accompanies the RNA from the gene through the nuclear pores and into polysomes. Cell, 84: 253-264.
137. Wahle, E., and Keller, W. 1996. The biochemistry of poly-adenylation. Trends Biochem. Sci. 21: 247-250.
138. Wang, J., and Manley, J. L. 1995. Overexpression of the SR proteins ASF/SF2 and SC35 influences alternative splicing in vivo in diverse ways. RNA. 1: 346-355.
139. Wang, Z., Hoffmann, H.M., and Grabowski, P. J. 1995. Intrinsic U2AF binding is modulated by exon enhancer signals in parallel with changes in-splicing activity. RNA, 1: 21-35.
140. Wang, H.Y., Lin, W., Dyck, J.A., Yeakley, J. M., Songyang, Z., Cantley, L.C., and Fu, X.D. 1998. SRPK2: a differentially expressed SR protein-specific kinase involved in mediating the interaction and localization of pre-mRNA splicing factors in mammalian cells. J. Cell Biol. 140: 737-750.
141. Will, C., and Luhrmann, R. 1997. snRNP structure and function. IRL Press, Oxford.
142. Woppmann, A., Will, C.L., Kornstadt, U., Zuo, P., Manley, J.L., and Luhrmann, R. 1993. Identification of an snRNP-associated kinase activity that phosphorylates arginine/serine rich domains typical of splicing factors. Nucleic Acids Res. 21: 2815-2822.
143. Wu, J.Y., and Maniatis, T. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell. 75: 1061-1070.
144. Xiao, S.H., and Manley, J.L. 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.
145. Xiao, S.H., and Manley, J.L. 1998. Phosphorylation-dephosphorylation differentially affects activities of splicing factor ASF/SF2. EMBO J. 17: 6359-6367.
146. Yeakley, J.M., Tronchere, H., Olesen, J., Dyck, J.A., Wang, H.Y., and Fu, X. D. 1999. Phosphorylation regulates in vivo interaction and molecular targeting of serine/arginine-rich pre-mRNA splicing factors. J. Cell Biol. 145: 447-455.
147. Yuryev, A., Patturajan, M., Litingtung, Y., Joshi, R.V., Gentile, C., Gebara, M., and Corden, J.L. 1996. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl. Acad. Sci. U.S.A. 93: 6975-6980.
148. Zahler, A.M., Lane, W.S., Stolk, J.A., and Roth, M.B. 1992. SR proteins: a conserved family of pre-mRNA splicing factors. Genes Dev. 6: 837-847.
149. Zahler, A.M., Neugebauer, K.M., Lane, W.S., and Roth, M.B. 1993a. Distinct functions of SR proteins in alternative splicing. Science (Washington, D.C.), 260: 219-222.
150. Zahler, A.M., Neugebauer, K.M., Stolk, J.A., and Roth, M.B. 1993b. Human SR proteins and isolation of a cDNA encoding SRp75. Mol. Cell. Biol. 13: 4023-4028.
151. Zamore, P.D., and Green, M.R. 1991. Biochemical characterization of U2 snRNP auxiliary factor: an essential pre-mRNA splicing factor with a novel intranuclear distribution. EMBO J. 10: 207-214.
152. Zamore, P.D., Patton, J.G., and Green, M.R. 1992. Cloning and domain structure of the mammalian splicing factor U2AF. Nature (London), 355: 609-614.
153. Zeitlin, S., Parent, A., Silverstein, S., and Efstratiatdis, A. 1987. Pre-mRNA splicing and the nuclear matrix. Mol. Cell. Biol. 7: 111-120.
154. Zhang, W.J., and Wu, J.Y. 1996. Functional properties of p54, a novel SR protein active in constitutive and alternative splicing. Mol. Cell Biol. 16: 5400-5408.
155. Zhang, W.J., and Wu, J.Y. 1998. Sip 1, a novel RS domain-containing protein essential for pre-mRNA splicing. Mol. Cell Biol. 18: 676-684.
156. Zhang, M., Zamore, P.D., Carmo-Fonseca, M., Lamond, A.I., and Green, M.R. 1992. Cloning and intracellular localization of the U2 small nuclear ribonucleoprotein auxiliary factor small subunit. Proc. Natl. Acad. Sci. U.S.A. 89: 8769-8773.
157. Zuo, P., and Maniatis, T. 1996. The splicing factor U2AF35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. Genes Dev. 10: 1356-1368.