Broad Specificity of SR (Serine{plus 45 degree rule}Arginine) Proteins in the Regulation of Alternative Splicing of Pre-Messenger RNA

Progress in Nucleic Acid Research and Molecular Biology

Volumn 78, Issue , 2004, Pages 37-88

  Bourgeois, Cyril F ^a   Lejeune, Fabrice ^b   Stévenin, James ^a  

^a CNRS   (France)

^b UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN; RNA PRECURSOR;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ANIMAL; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; ENHANCER REGION; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; REVIEW; RNA SPLICING; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; ENHANCER ELEMENTS (GENETICS); HUMANS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; RNA PRECURSORS; RNA SPLICING; RNA-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SIGNAL TRANSDUCTION;

EID: 14644431487     PISSN: 00796603     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0079-6603(04)78002-2     Document Type: Article

References (238)

1. C.B. Burge T. Tuschl P.A. Sharp Splicing of precursors to messenger RNAs by the spliceosome R.F. Gesteland T.R. Cech J.F. Atkins “The RNA World II” 1999 Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York 525 560
2. M.S. Jurica M.J. Moore Pre-mRNA splicing: Awash in a sea of proteins Mol. Cell 12 2003 5 14
3. B.R. Graveley Sorting out the complexity of SR protein functions RNA 6 2000 1197 1211
4. J.R. Sanford D. Longman J.F. Caceres Multiple roles of the SR protein family in splicing regulation Prog. Mol. Subcell. Biol. 31 2003 33 58
5. G.C. Roberts C.W. Smith Alternative splicing: Combinatorial output from the genome Curr. Opin. Chem. Biol. 6 2002 375 383
6. B. Modrek C. Lee A genomic view of alternative splicing Nat. Genet. 30 2002 13 19
7. A.J. Lopez Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation Annu. Rev. Genet. 32 1998 279 305
8. B.J. Blencowe Exonic splicing enhancers: Mechanism of action, diversity and role in human genetic diseases Trends Biochem. Sci. 25 2000 106 110
9. B.R. Graveley Alternative splicing: Increasing diversity in the proteomic world Trends Genet. 17 2001 100 107
10. T. Maniatis B. Tasic Alternative pre-mRNA splicing and proteome expansion in metazoans Nature 418 2002 236 243
11. J.F. Caceres A.R. Kornblihtt Alternative splicing: Multiple control mechanisms and involvement in human disease Trends Genet. 18 2002 186 193
12. R. Tacke J.L. Manley Determinants of SR protein specificity Curr. Opin. Cell. Biol. 11 1999 358 362
13. A.R. Krainer G.C. Conway D. Kozak The essential pre-mRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites Cell 62 1990 35 42
14. A.R. Krainer G.C. Conway D. Kozak Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells Genes Dev. 4 1990 1158 1171
15. H. Ge J.L. Manley A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro Cell 62 1990 25 34
16. H. Ge P. Zuo J.L. Manley Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators Cell 66 1991 373 382
17. X.D. Fu T. Maniatis Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus Nature 343 1990 437 441
18. X.D. Fu A. Mayeda T. Maniatis A.R. Krainer 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. USA 89 1992 11224 11228
19. A.M. Zahler W.S. Lane J.A. Stolk M.B. Roth SR proteins: A conserved family of pre-mRNA splicing factors Genes Dev. 6 1992 837 847
20. A.M. Zahler K.M. Neugebauer J.A. Stolk M.B. Roth Human SR proteins and isolation of a cDNA encoding SRp75 Mol. Cell. Biol. 13 1993 4023 4028
21. Y. Cavaloc M. Popielarz J.P. Fuchs R. Gattoni J. Stevenin Characterization and cloning of the human splicing factor 9G8: A novel 35 kDa factor of the serine⧸arginine protein family EMBO J. 13 1994 2639 2649
22. W.J. Zhang J.Y. Wu Functional properties of p54, A novel SR protein active in constitutive and alternative splicing Mol. Cell. Biol. 16 1996 5400 5408
23. G.R. Screaton J.F. Caceres A. Mayeda M.V. Bell M. Plebanski D.G. Jackson J.I. Bell A.R. Krainer Identification and characterization of three members of the human SR family of pre-mRNA splicing factors EMBO J. 14 1995 4336 4349
24. J. Soret R. Gattoni C. Guyon A. Sureau M. Popielarz E. Le Rouzic S. Dumon F. Apiou B. Dutrillaux H. Voss W. Ansorge J. Stevenin B. Perbal Characterization of SRp46, a novel human SR splicing factor encoded by a PR264⧸SC35 retropseudogene Mol. Cell. Biol. 18 1998 4924 4934
25. L. Boucher C.A. Ouzounis A.J. Enright B.J. Blencowe A genome-wide survey of RS domain proteins RNA 7 2001 1693 1701
26. B.J. Blencowe J.A. Bowman S. McCracken E. Rosonina SR-related proteins and the processing of messenger RNA precursors Biochem. Cell Biol. 77 1999 277 291
27. E. Labourier H.M. Bourbon I.E. Gallouzi M. Fostier E. Allemand J. Tazi Antagonism between RSF1 and SR proteins for both splice-site recognition in vitro and Drosophila development Genes Dev. 13 1999 740 753
28. D.C. Barnard J.G. Patton Identification and characterization of a novel serine-arginine-rich splicing regulatory protein Mol. Cell. Biol. 20 2000 3049 3057
29. A.E. Cowper J.F. Caceres A. Mayeda G.R. Screaton Serine-arginine (SR) protein-like factors that antagonize authentic SR proteins and regulate alternative splicing J. Biol. Chem. 276 2001 48908 48914
30. C. Shin J.L. Manley The SR protein SRp38 represses splicing in M phase cells Cell 111 2002 407 417
31. J.D. Kohtz Protein–protein interactions and 5′-splice-site recognition in mammalian mRNA precursors Nature 368 1994 119 124
32. D. Staknis R. Reed 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 1994 7670 7682
33. P. Zuo T. Maniatis The splicing factor U2AF35 mediates critical protein–protein interactions in constitutive and enhancer-dependent splicing Genes Dev. 10 1996 1356 1368
34. S.M. Berget Exon recognition in vertebrate splicing J. Biol. Chem. 270 1995 2411 2414
35. K.J. Hertel T. Maniatis Serine-arginine (SR)-rich splicing factors have an exon-independent function in pre-mRNA splicing Proc. Natl. Acad. Sci. USA 96 1999 2651 2655
36. R.F. Roscigno M.A. Garcia-Blanco SR proteins escort the U4⧸U6.U5 tri-snRNP to the spliceosome RNA 1 1995 692 706
37. S. Teigelkamp C. Mundt T. Achsel C.L. Will R. Luhrmann 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 1997 1313 1326
38. S. Fetzer J. Lauber C.L. Will R. Luhrmann The [U4⧸U6.U5] tri-snRNP-specific 27K protein is a novel SR protein that can be phosphorylated by the snRNP-associated protein kinase RNA 3 1997 344 355
39. O.V. Makarova E.M. Makarov R. Luhrmann The 65 and 110 kDa SR-related proteins of the U4⧸U6.U5 tri-snRNP are essential for the assembly of mature spliceosomes EMBO J. 20 2001 2553 2563
40. S. Furuyama J.P. Bruzik Multiple roles for SR proteins in trans splicing Mol. Cell. Biol. 22 2002 5337 5346
41. J. Zhu A.R. Krainer Pre-mRNA splicing in the absence of an SR protein RS domain Genes Dev. 14 2000 3166 3178
42. B.R. Graveley K.J. Hertel T. Maniatis The role of U2AF35 and U2AF65 in enhancer-dependent splicing RNA 7 2001 806 818
43. S. Guth T.O. Tange E. Kellenberger J. Valcarcel Dual function for U2AF(35) in AG-dependent pre-mRNA splicing Mol. Cell. Biol. 21 2001 7673 7681
44. A.G. Eldridge Y. Li P.A. Sharp B.J. Blencowe The SRm160⧸300 splicing coactivator is required for exon-enhancer function Proc. Natl. Acad. Sci. USA 96 1999 6125 6130
45. J.L. Kan M.R. Green Pre-mRNA splicing of IgM exons M1 and M2 is directed by a juxtaposed splicing enhancer and inhibitor Genes Dev. 13 1999 462 471
46. J. Zhu A. Mayeda A.R. Krainer Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins Mol. Cell 8 2001 1351 1361
47. J.Y. Wu T. Maniatis Specific interactions between proteins implicated in splice site selection and regulated alternative splicing Cell 75 1993 1061 1070
48. I.C. Eperon Selection of alternative 5′ splice sites: Role of U1 snRNP and models for the antagonistic effects of SF2⧸ASF and hnRNP A1 Mol. Cell. Biol. 20 2000 8303 8318
49. A. Mayeda A.R. Krainer Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2 Cell 68 1992 365 375
50. L.L. Elrick M.B. Humphrey T.A. Cooper S.M. Berget A short sequence within two purine-rich enhancers determines 5′ splice site specificity Mol. Cell. Biol. 18 1998 343 352
51. V. Heinrichs L.C. Ryner B.S. Baker Regulation of sex-specific selection of fruitless 5′ splice sites by transformer and transformer-2 Mol. Cell. Biol. 18 1998 450 458
52. C.F. Bourgeois M. Popielarz G. Hildwein J. Stevenin Identification of a bidirectional splicing enhancer: Differential involvement of SR proteins in 5′ or 3′ splice site activation Mol. Cell. Biol. 19 1999 7347 7356
53. M. Selvakumar D.M. Helfman Exonic splicing enhancers contribute to the use of both 3′ and 5′ splice site usage of rat beta-tropomyosin pre-mRNA RNA 5 1999 378 394
54. J. Cote M.J. Simard B. Chabot An element in the 5′ common exon of the NCAM alternative splicing unit interacts with SR proteins and modulates 5′ splice site selection Nucleic Acids Res. 27 1999 2529 2537
55. F. Lejeune Y. Cavaloc J. Stevenin Alternative splicing of intron 3 of the serine⧸arginine-rich protein 9G8 gene: Identification of flanking exonic splicing enhancers and involvement of 9G8 as a trans -acting factor J. Biol. Chem. 276 2001 7850 7858
56. B.J. Lam Enhancer-dependent 5′-splice site control of fruitless pre-mRNA splicing J. Biol. Chem. 278 2003 22740 22747
57. Y. Huang J.A. Steitz Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA Mol. Cell 7 2001 899 905
58. R. Lemaire Stability of a PKCI-1-related mRNA is controlled by the splicing factor ASF⧸SF2: A novel function for SR proteins Genes Dev. 16 2002 594 607
59. Y. Huang R. Gattoni J. Stevenin J.A. Steitz SR splicing factors serve as adapter proteins for TAP-dependent mRNA export Mol. Cell. 11 2003 837 843
60. T. Misteli RNA splicing: What has phosphorylation got to do with it? Curr. Biol. 9 1999 R198 R200
61. J. Soret J. Tazi Phosphorylation-dependent control of the pre-mRNA splicing machinery Prog. Mol. Subcell. Biol. 31 2003 89 126
62. J.F. Gui W.S. Lane X.D. Fu A serine kinase regulates intracellular localization of splicing factors in the cell cycle Nature 369 1994 678 682
63. H.Y. Wang 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 1998 737 750
64. K. Colwill The Clk⧸Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution EMBO J. 15 1996 265 275
65. O. Nayler S. Stamm A. Ullrich Characterization and comparison of four serine- and arginine-rich (SR) protein kinases Biochem. J. 326 1997 693 700
66. K. Colwill SRPK1 and Clk⧸Sty protein kinases show distinct substrate specificities for serine⧸arginine-rich splicing factors J. Biol. Chem. 271 1996 24569 24575
67. F. Rossi Specific phosphorylation of SR proteins by mammalian DNA topoisomerase I Nature 381 1996 80 82
68. B. Pilch Specific inhibition of serine- and arginine-rich splicing factors phosphorylation, spliceosome assembly, and splicing by the antitumor drug NB-506 Cancer Res. 61 2001 6876 6884
69. J.F. Caceres A.R. Krainer Functional analysis of pre-mRNA splicing factor SF2⧸ASF structural domains EMBO J. 12 1993 4715 4726
70. P. Zuo J.L. Manley Functional domains of the human splicing factor ASF⧸SF2 EMBO J. 12 1993 4727 4737
71. S.H. Xiao J.L. Manley Phosphorylation of the ASF⧸SF2 RS domain affects both protein–protein and protein–RNA interactions and is necessary for splicing Genes Dev. 11 1997 334 344
72. M. Perutz Polar zippers: Their role in human disease Protein Sci. 3 1994 1629 1637
73. W. Cao S.F. Jamison M.A. Garcia-Blanco Both phosphorylation and dephosphorylation of ASF⧸SF2 are required for pre-mRNA splicing in vitro RNA 3 1997 1456 1467
74. S.D. Chandler A. Mayeda J.M. Yeakley A.R. Krainer X.D. Fu RNA splicing specificity determined by the coordinated action of RNA recognition motifs in SR proteins Proc. Natl. Acad. Sci. USA 94 1997 3596 3601
75. W. van Der Houven Van Oordt K. Newton G.R. Screaton J.F. Caceres Role of SR protein modular domains in alternative splicing specificity in vivo Nucleic Acids Res. 28 2000 4822 4831
76. J. Wang S.H. Xiao J.L. Manley Genetic analysis of the SR protein ASF⧸SF2: Interchangeability of RS domains and negative control of splicing Genes Dev. 12 1998 2222 2233
77. B.R. Graveley T. Maniatis Arginine⧸serine-rich domains of SR proteins can function as activators of pre-mRNA splicing Mol. Cell 1 1998 765 771
78. B.R. Graveley K.J. Hertel T. Maniatis A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers EMBO J. 17 1998 6747 6756
79. E. Allemand Distinctive features of Drosophila alternative splicing factor RS domain: Implication for specific phosphorylation, shuttling, and splicing activation Mol. Cell. Biol. 21 2001 1345 1359
80. A.M. Krecic M.S. Swanson hnRNP complexes: Composition, structure, and function Curr. Opin. Cell. Biol. 11 1999 363 371
81. G. Dreyfuss V.N. Kim N. Kataoka Messenger-RNA-binding proteins and the messages they carry Nat. Rev. Mol. Cell. Biol. 3 2002 195 205
82. Y. Cavaloc C.F. Bourgeois L. Kister J. Stevenin The splicing factors 9G8 and SRp20 transactivate splicing through different and specific enhancers RNA 5 1999 468 483
83. S. Lopato R. Gattoni G. Fabini J. Stevenin A. Barta A novel family of plant splicing factors with a Zn knuckle motif: Examination of RNA binding and splicing activities Plant Mol. Biol. 39 1999 761 773
84. G. Varani K. Nagai RNA recognition by RNP proteins during RNA processing Annu. Rev. Biophys. Biomol. Struct. 27 1998 407 445
85. N. Handa Structural basis for recognition of the tra mRNA precursor by the sex-lethal protein Nature 398 1999 579 585
86. F.H. Allain P. Bouvet T. Dieckmann J. Feigon Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin EMBO J. 19 2000 6870 6881
87. S.G. Nadler Interactions of the A1 heterogeneous nuclear ribonucleoprotein and its proteolytic derivative, UP1, with RNA and DNA: Evidence for multiple RNA binding domains and salt-dependent binding mode transitions Biochemistry 30 1991 2968 2976
88. C.G. Burd G. Dreyfuss RNA binding specificity of hnRNP A1: Significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing EMBO J. 13 1994 1197 1204
89. M. Caputi A.M. Zahler Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H⧸H′⧸F⧸2H9 family J. Biol. Chem. 276 2001 43850 43859
90. D.J. Kenan C.C. Query J.D. Keene RNA recognition: Towards identifying determinants of specificity Trends Biochem. Sci. 16 1991 214 220
91. R. Tacke J.L. Manley The human splicing factors ASF⧸SF2 and SC35 possess distinct, functionally significant RNA binding specificities EMBO J. 14 1995 3540 3551
92. E. Birney S. Kumar A.R. Krainer Analysis of the RNA-recognition motif and RS and RGG domains: Conservation in metazoan pre-mRNA splicing factors Nucleic Acids Res. 21 1993 5803 5816
93. J. Wang Y. Takagaki J.L. Manley Targeted disruption of an essential vertebrate gene: ASF⧸SF2 is required for cell viability Genes Dev. 10 1996 2588 2599
94. A. Mittermaier L. Varani D.R. Muhandiram L.E. Kay G. Varani Changes in side-chain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein J. Mol. Biol. 294 1999 967 979
95. X.D. Fu Specific commitment of different pre-mRNAs to splicing by single SR proteins Nature 365 1993 82 85
96. A.M. Zahler K.M. Neugebauer W.S. Lane M.B. Roth Distinct functions of SR proteins in alternative pre-mRNA splicing Science 260 1993 219 222
97. A. Watakabe K. Tanaka Y. Shimura The role of exon sequences in splice site selection Genes Dev. 7 1993 407 418
98. Q. Sun A. Mayeda R.K. Hampson A.R. Krainer F.M. Rottman General splicing factor SF2⧸ASF promotes alternative splicing by binding to an exonic splicing enhancer Genes Dev. 7 1993 2598 2608
99. A. Lavigueur H. La Branche A.R. Kornblihtt B. Chabot A splicing enhancer in the human fibronectin alternate ED1 exon interacts with SR proteins and stimulates U2 snRNP binding Genes Dev. 7 1993 2405 2417
100. M. Tian T. Maniatis A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA Cell 74 1993 105 114
101. C. Tuerk L. Gold Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249 1990 505 510
102. H. Tian R. Kole Selection of novel exon recognition elements from a pool of random sequences Mol. Cell. Biol. 15 1995 6291 6298
103. H.X. Liu M. Zhang A.R. Krainer Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins Genes Dev. 12 1998 1998 2012
104. H.X. Liu S.L. Chew L. Cartegni M.Q. Zhang A.R. Krainer Exonic splicing enhancer motif recognized by human SC35 under splicing conditions Mol. Cell. Biol. 20 2000 1063 1071
105. T.D. Schaal T. Maniatis Multiple distinct splicing enhancers in the protein-coding sequences of a constitutively spliced pre-mRNA Mol. Cell. Biol. 19 1999 261 273
106. V. Heinrichs B.S. Baker The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences EMBO J. 14 1995 3987 4000
107. R. Tacke Y. Chen J.L. Manley 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 1997 1148 1153
108. H. Shi B.E. Hoffman J.T. Lis A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52 Mol. Cell. Biol. 17 1997 2649 2657
109. R. Tacke M. Tohyama S. Ogawa J.L. Manley Human Tra2 proteins are sequence-specific activators of pre-mRNA splicing Cell 93 1998 139 148
110. B.G. Yue G. Akusjarvi A downstream splicing enhancer is essential for in vitro pre-mRNA splicing FEBS Lett. 451 1999 10 14
111. E. Stickeler The RNA binding protein YB-1 binds A⧸C-rich exon enhancers and stimulates splicing of the CD44 alternative exon v4 EMBO J. 20 2001 3821 3830
112. L. Cartegni J. Wang Z. Zhu M.Q. Zhang A.R. Krainer ESEfinder: A web resource to identify exonic splicing enhancers Nucleic Acids Res. 31 2003 3568 3571
113. L.A. Boukis J.P. Bruzik Functional selection of splicing enhancers that stimulate trans -splicing in vitro RNA 7 2001 793 805
114. T.D. Schaal T. Maniatis Selection and characterization of pre-mRNA splicing enhancers: Identification of novel SR protein-specific enhancer sequences Mol. Cell. Biol. 19 1999 1705 1719
115. M.E. Gallego R. Gattoni J. Stevenin J. Marie A. Expert-Bezancon The SR splicing factors ASF⧸SF2 and SC35 have antagonistic effects on intronic enhancer dependent splicing of the beta-tropomyosin alternative exon 6A EMBO J. 16 1997 1772 1784
116. A. Mayeda G.R. Screaton S.D. Chandler X.D. Fu A.R. Krainer Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements Mol. Cell. Biol. 19 1999 1853 1863
117. M. Caputi A.M. Zahler SR proteins and hnRNP H regulate the splicing of the HIV-1 tev-specific exon 6D EMBO J. 21 2002 845 855
118. S. Guil Roles of hnRNP A1, SR proteins, and p68 helicase in c-H-ras alternative splicing regulation Mol. Cell. Biol. 23 2003 2927 2941
119. D. Galiana-Arnoux The CD44 alternative v9 exon contains a splicing enhancer responsive to the SR proteins 9G8, ASF⧸SF2 and SRp20 J. Biol. Chem. 278 2003 32943 32953
120. H. Lou K.M. Neugebauer R.F. Gagel S.M. Berget Regulation of alternative polyadenylation by U1 snRNPs and SRp20 Mol. Cell. Biol. 18 1998 4977 4985
121. K.W. Lynch T. Maniatis Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer Genes Dev. 10 1996 2089 2101
122. J. Ramchatesingh A.M. Zahler K.M. Neugebauer M.B. Roth T.A. Cooper 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 1995 4898 4907
123. K. Du Y. Peng L.E. Greenbaum B.A. Haber R. Taub HRS⧸SRp40-mediated inclusion of the fibronectin EIIIB exon, a possible cause of increased EIIIB expression in proliferating liver Mol. Cell. Biol. 17 1997 4096 4104
124. B.A. Kuo P.A. Norton Accurate selection of a 5′ splice site requires sequences within fibronectin alternative exon B Nucleic Acids Res. 27 1999 3945 3952
125. Q. Tran J.R. Roesser SRp55 is a regulator of calcitonin⧸CGRP alternative RNA splicing Biochemistry 42 2003 951 957
126. X. Li M.E. Shambaugh F.M. Rottman J.A. Bokar SR proteins ASF⧸SF2 and 9G8 interact to activate enhancer-dependent intron D splicing of bovine growth hormone pre-mRNA in vitro RNA 6 2000 1847 1858
127. D. Longman I.L. Johnstone J.F. Caceres Functional characterization of SR and SR-related genes in Caenorhabditis elegans EMBO J. 19 2000 1625 1637
128. W.G. Fairbrother R.F. Yeh P.A. Sharp C.B. Burge Predictive identification of exonic splicing enhancers in human genes Science 297 2002 1007 1013
129. M. Caputi R.J. Kendzior Jr. K.L. Beemon A nonsense mutation in the fibrillin-1 gene of a Marfan syndrome patient induces NMD and disrupts an exonic splicing enhancer Genes Dev. 16 2002 1754 1759
130. L. Cartegni A.R. Krainer Disruption of an SF2⧸ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1 Nat. Genet. 30 2002 377 384
131. P.J. Smith An exonic splicing enhancer in human IGF-I pre-mRNA mediates recognition of alternative exon 5 by the serine-arginine protein splicing factor-2⧸alternative splicing factor Endocrinology 143 2002 146 154
132. F. Pagani E. Buratti C. Stuani F.E. Baralle Missense, nonsense, and neutral mutations define juxtaposed regulatory elements of splicing in cystic fibrosis transmembrane regulator exon 9 J. Biol. Chem. 278 2003 26580 26588
133. I. D'Souza G.D. Schellenberg Determinants of 4-repeat tau expression: Coordination between enhancing and inhibitory splicing sequences for exon 10 inclusion J. Biol. Chem. 275 2000 17700 17709
134. H.X. Liu L. Cartegni M.Q. Zhang A.R. Krainer A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes Nat. Genet. 27 2001 55 58
135. Z. Jiang Mutations in tau gene exon 10 associated with FTDP-17 alter the activity of an exonic splicing enhancer to interact with Tra2 beta J. Biol. Chem. 278 2003 18997 19007
136. M. Mine Splicing error in E1 alpha pyruvate dehydrogenase mRNA caused by novel intronic mutation responsible for lactic acidosis and mental retardation J. Biol. Chem. 278 2003 11768 11772
137. L. Cartegni S.L. Chew A.R. Krainer Listening to silence and understanding nonsense: Exonic mutations that affect splicing Nat. Rev. Genet. 3 2002 285 298
138. H. Amrein M.L. Hedley T. Maniatis The role of specific protein–RNA and protein–protein interactions in positive and negative control of pre-mRNA splicing by transformer 2 Cell 76 1994 735 746
139. D.S. Chandler J. Qi W. Mattox Direct repression of splicing by transformer-2 Mol. Cell. Biol. 23 2003 5174 5185
140. R. Tacke J.L. Manley Functions of SR and Tra2 proteins in pre-mRNA splicing regulation Proc. Soc. Exp. Biol. Med. 220 1999 59 63
141. Y. Hofmann C.L. Lorson S. Stamm E.J. Androphy B. Wirth Htra2-beta 1 stimulates an exonic splicing enhancer and can restore full-length SMN expression to survival motor neuron 2 (SMN2) Proc. Natl. Acad. Sci. USA 97 2000 9618 9623
142. M.T. Nasim T.K. Chernova H.M. Chowdhury B.G. Yue I.C. Eperon HnRNP G and Tra2beta: Opposite effects on splicing matched by antagonism in RNA binding Hum. Mol. Genet. 12 2003 1337 1348
143. L. Yang L.J. Embree S. Tsai D.D. Hickstein Oncoprotein TLS interacts with serine–arginine proteins involved in RNA splicing J. Biol. Chem. 273 1998 27761 27764
144. E. Labourier Recognition of exonic splicing enhancer sequences by the Drosophila splicing repressor RSF1 Nucleic Acids Res. 27 1999 2377 2386
145. L. Yang L.J. Embree D.D. Hickstein TLS-ERG leukemia fusion protein inhibits RNA splicing mediated by serine–arginine proteins Mol. Cell. Biol. 20 2000 3345 3354
146. D.C. Barnard J. Li R. Peng J.G. Patton Regulation of alternative splicing by SRrp86 through coactivation and repression of specific SR proteins RNA 8 2002 526 533
147. J. Venables I. Eperon The roles of RNA-binding proteins in spermatogenesis and male infertility Curr. Opin. Genet. Dev. 9 1999 346 354
148. J.P. Venables Alternative splicing in the testes Curr. Opin. Genet. Dev. 12 2002 615 619
149. D.J. Elliott An evolutionarily conserved germ cell-specific hnRNP is encoded by a retrotransposed gene Hum. Mol. Genet. 9 2000 2117 2124
150. D.J. Elliott C.F. Bourgeois A. Klink J. Stevenin H.J. Cooke A mammalian germ cell-specific RNA-binding protein interacts with ubiquitously expressed proteins involved in splice site selection Proc. Natl. Acad. Sci. USA 97 2000 5717 5722
151. J.P. Venables RBMY, a probable human spermatogenesis factor, and other hnRNP G proteins interact with Tra2beta and affect splicing Hum. Mol. Genet. 9 2000 685 694
152. Y. Hofmann B. Wirth hnRNP-G promotes exon 7 inclusion of survival motor neuron (SMN) via direct interaction with Htra2-betal Hum. Mol. Genet. 11 2002 2037 2049
153. K.W. Lynch T. Maniatis Synergistic interactions between two distinct elements of a regulated splicing enhancer Genes Dev. 9 1995 284 293
154. B.J. Blencowe R. Issner J.A. Nickerson P.A. Sharp A coactivator of pre-mRNA splicing Genes Dev. 12 1998 996 1009
155. B.J. Blencowe The SRm160⧸300 splicing coactivator subunits RNA 6 2000 111 120
156. D. Longman Multiple interactions between SRm160 and SR family proteins in enhancer-dependent splicing and development of C. elegans Curr. Biol. 11 2001 1923 1933
157. H. Le Hir E. Izaurralde L.E. Maquat M.J. Moore The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon–exon junctions EMBO J. 19 2000 6860 6869
158. B.R. Szymczyna Structure and function of the PWI motif: A novel nucleic acid-binding domain that facilitates pre-mRNA processing Genes Dev. 17 2003 461 475
159. A.R. Krainer A. Mayeda D. Kozak G. Binns Functional expression of cloned human splicing factor SF2: Homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators Cell 66 1991 383 394
160. S.K. PetersenMahrt The splicing factor-associated protein, p32, regulates RNA splicing by inhibiting ASF⧸SF2 RNA binding and phosphorylation EMBO J. 18 1999 1014 1024
161. H.C. van Leeuwen P. O'Hare Retargeting of the mitochondrial protein p32⧸gC1Qr to a cytoplasmic compartment and the cell surface J. Cell. Sci. 114 2001 2115 2123
162. H.Y. Wang X. Xu J.H. Ding J.R. Bermingham Jr. X.D. Fu SC35 plays a role in T cell development and alternative splicing of CD45 Mol. Cell 7 2001 331 342
163. C. Ghigna M. Moroni C. Porta S. Riva G. Biamonti Altered expression of heterogeneous nuclear ribonucleoproteins and SR factors in human colon adenocarcinomas Cancer Res. 58 1998 5818 5824
164. E. Stickeler F. Kittrell D. Medina S.M. Berget Stage-specific changes in SR splicing factors and alternative splicing in mammary tumorigenesis Oncogene 18 1999 3574 3582
165. R.H. Diamond Novel delayed-early and highly insulin-induced growth response genes: Identification of HRS, a potential regulator of alternative pre-mRNA splicing J. Biol. Chem. 268 1993 15185 15192
166. L.P. Lim P.A. Sharp Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats Mol. Cell. Biol. 18 1998 3900 3906
167. M. Vellard A. Sureau J. Soret C. Martinerie B. Perbal A potential splicing factor is encoded by the opposite strand of the trans -spliced c-myb exon Proc. Natl. Acad. Sci. USA 89 1992 2511 2515
168. M. Popielarz Y. Cavaloc M.G. Mattei R. Gattoni J. Stevenin The gene encoding human splicing factor 9G8: Structure, chromosomal localization, and expression of alternatively processed transcripts J. Biol. Chem. 270 1995 17830 17835
169. H. Jumaa J.L. Guenet P.J. Nielsen Regulated expression and RNA processing of transcripts from the Srp20 splicing factor gene during the cell cycle Mol. Cell. Biol. 17 1997 3116 3124
170. H. Jumaa P.J. Nielsen The splicing factor SRp20 modifies splicing of its own mRNA and ASF⧸SF2 antagonizes this regulation EMBO J. 16 1997 5077 5085
171. A. Sureau R. Gattoni Y. Dooghe J. Stevenin J. Soret SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs EMBO J. 20 2001 1785 1796
172. M.C. Lai R.I. Lin W.Y. Tarn Differential effects of hyperphosphorylation on splicing factor SRp55 Biochem. J. 371 2003 937 945
173. J. Prasad K. Colwill T. Pawson J.L. Manley The protein kinase Clk⧸Sty directly modulates SR protein activity: Both hyper- and hypophosphorylation inhibit splicing Mol. Cell. Biol. 19 1999 6991 7000
174. J.F. Caceres G.R. Screaton A.R. Krainer A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm Genes Dev. 12 1998 55 66
175. T. Misteli Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo J. Cell. Biol. 143 1998 297 307
176. S. Stamm Signals and their transduction pathways regulating alternative splicing: A new dimension of the human genome Hum. Mol. Genet. 11 2002 2409 2416
177. R. Daoud Ischemia induces a translocation of the splicing factor tra2-beta 1 and changes alternative splicing patterns in the brain J. Neurosci. 22 2002 5889 5899
178. Z.H. Jiang W.J. Zhang Y. Rao J.Y. Wu Regulation of Ich-1 pre-mRNA alternative splicing and apoptosis by mammalian splicing factors Proc. Natl. Acad. Sci. USA 95 1998 9155 9160
179. N.A. Patel Insulin regulates alternative splicing of protein kinase C beta II through a phosphatidylinositol 3-kinase-dependent pathway involving the nuclear serine⧸arginine-rich splicing factor, SRp40, in skeletal muscle cells J. Biol. Chem. 276 2001 22648 22654
180. X. Liu A. Mayeda M. Tao Z.M. Zheng Exonic splicing enhancer-dependent selection of the bovine papillomavirus type 1 nucleotide 3225 3′ splice site can be rescued in a cell lacking splicing factor ASF⧸SF2 through activation of the phosphatidylinositol 3-kinase⧸Akt pathway J. Virol. 77 2003 2105 2115
181. T. Obata Peptide and protein library screening defines optimal substrate motifs for AKT⧸PKB J. Biol. Chem. 275 2000 36108 36115
182. C.E. Chalfant FAS activation induces dephosphorylation of SR proteins: Dependence on the de novo generation of ceramide and activation of protein phosphatase 1 J. Biol. Chem. 276 2001 44848 44855
183. C.E. Chalfant De novo ceramide regulates the alternative splicing of caspase 9 and Bcl-x in A549 lung adenocarcinoma cells: Dependence on protein phosphatase-1 J. Biol. Chem. 277 2002 12587 12595
184. J.E. Mermoud P.T. Cohen A.I. Lamond Regulation of mammalian spliceosome assembly by a protein phosphorylation mechanism EMBO J. 13 1994 5679 5688
185. G.M. Jenkins Acute activation of de novo sphingolipid biosynthesis upon heat shock causes an accumulation of ceramide and subsequent dephosphorylation of SR proteins J. Biol. Chem. 277 2002 42572 42578
186. M. Denegri Stress-induced nuclear bodies are sites of accumulation of pre-mRNA processing factors Mol. Biol. Cell 12 2001 3502 3514
187. G. Akusjarvi J. Stevenin Remodelling of the host cell RNA splicing machinery during an adenovirus infection Curr. Top. Microbiol. Immunol. 272 2003 253 286
188. A. Kanopka O. Muhlemann G. Akusjarvi Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA Nature 381 1996 535 538
189. M. Himmelspach Y. Cavaloc K. Chebli J. Stevenin R. Gattoni Titration of serine⧸arginine (SR) splicing factors during adenoviral infection modulates E1A pre-mRNA alternative splicing RNA 1 1995 794 806
190. A. Kanopka Regulation of adenovirus alternative RNA splicing by dephosphorylation of SR proteins Nature 393 1998 185 187
191. C. Estmer Nilsson The adenovirus E4-ORF4 splicing enhancer protein interacts with a subset of phosphorylated SR proteins EMBO J. 20 2001 864 871
192. T.S. Huang C.E. Nilsson T. Punga G. Akusjarvi Functional inactivation of the SR family of splicing factors during a vaccinia virus infection EMBO Rep. 3 2002 1088 1093
193. K.S. Sciabica Q.J. Dai R.M. Sandri-Goldin ICP27 interacts with SRPK1 to mediate HSV splicing inhibition by altering SR protein phosphorylation EMBO J. 22 2003 1608 1619
194. A.C. Goldstrohm A.L. Greenleaf M.A. Garcia-Blanco Co-transcriptional splicing of pre-messenger RNAs: Considerations for the mechanism of alternative splicing Gene 277 2001 31 47
195. T. Maniatis R. Reed An extensive network of coupling among gene expression machines Nature 416 2002 499 506
196. K.M. Neugebauer On the importance of being co-transcriptional J. Cell Sci. 115 2002 3865 3871
197. K.J. Howe RNA polymerase II conducts a symphony of pre-mRNA processing activities Biochim. Biophys. Acta 1577 2002 308 324
198. N.J. Proudfoot A. Furger M.J. Dye Integrating mRNA processing with transcription Cell 108 2002 501 512
199. G. Nogues Control of alternative pre-mRNA splicing by RNA Pol II elongation: Faster is not always better IUBMB Life 55 2003 235 241
200. P. Cramer Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2⧸ASF and 9G8 effects on an exonic splicing enhancer [in process citation] Mol. Cell 4 1999 251 258
201. S. Kadener Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing EMBO J. 20 2001 5759 5768
202. S. Kadener J.P. Fededa M. Rosbash A.R. Kornblihtt Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation Proc. Natl. Acad. Sci. USA 99 2002 8185 8190
203. G. Nogues S. Kadener P. Cramer D. Bentley A.R. Kornblihtt Transcriptional activators differ in their abilities to control alternative splicing J. Biol. Chem. 277 2002 43110 43114
204. M. de la Mata A slow RNA polymerase II affects alternative splicing in vivo Mol. Cell 12 2003 525 532
205. D. Auboeuf A. Honig S.M. Berget B.W. O'Malley Coordinate regulation of transcription and splicing by steroid receptor coregulators Science 298 2002 416 419
206. F. Pagani C. Stuani E. Zuccato A.R. Kornblihtt F.E. Baralle Promoter architecture modulates CFTR exon 9 skipping J. Biol. Chem. 278 2003 1511 1517
207. A. Yuryev 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. USA 93 1996 6975 6980
208. J.L. Corden M. Patturajan A CTD function linking transcription to splicing Trends Biochem. Sci. 22 1997 413 416
209. H. Ge Y.Z. Si A.P. Wolffe A novel transcriptional coactivator, p52, functionally interacts with the essential splicing factor ASF⧸SF2 Mol. Cell 2 1998 751 759
210. L. Yang H.A. Chansky D.D. Hickstein EWS.Fli-1 fusion protein interacts with hyperphosphorylated RNA polymerase II and interferes with serine–arginine protein-mediated RNA splicing J. Biol. Chem. 275 2000 37612 37618
211. M. Meissner S. Lopato J. Gotzmann G. Sauermann A. Barta Proto-oncoprotein TLS⧸FUS is associated to the nuclear matrix and complexed with splicing factors PTB, SRm160, and SR proteins Exp. Cell Res. 283 2003 184 195
212. L.L. Knoop S.J. Baker EWS⧸FLI alters 5′-splice site selection J. Biol. Chem. 276 2001 22317 22322
213. A. Bertolotti Y. Lutz D.J. Heard P. Chambon L. Tora hTAF(II)68, a novel RNA⧸ssDNA-binding protein with homology to the pro-oncoproteins TLS⧸FUS and EWS is associated with both TFIID and RNA polymerase II EMBO J. 15 1996 5022 5031
214. A. Bertolotti EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: Interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes Mol. Cell. Biol. 18 1998 1489 1497
215. J.H. Trembley PITSLRE p110 protein kinases associate with transcription complexes and affect their activity J. Biol. Chem. 277 2002 2589 2596
216. D. Hu A. Mayeda J.H. Trembley J.M. Lahti V.J. Kidd CDK11 complexes promote pre-mRNA splicing J. Biol. Chem. 278 2003 8623 8629
217. P. Loyer J.H. Trembley J.M. Lahti V.J. Kidd The RNP protein, RNPS1, associates with specific isoforms of the p34cdc2-related PITSLRE protein kinase in vivo J. Cell Sci. 111 1998 1495 1506
218. A. Mayeda Purification and characterization of human RNPS1: A general activator of pre-mRNA splicing EMBO J. 18 1999 4560 4570
219. J. Lykke-Andersen M.D. Shu J.A. Steitz Communication of the position of exon–exon junctions to the mRNA surveillance machinery by the protein RNPS1 Science 293 2001 1836 1839
220. L.A. Dickinson A.J. Edgar J. Ehley J.M. Gottesfeld Cyclin L is an RS domain protein involved in pre-mRNA splicing J. Biol. Chem. 277 2002 25465 25473
221. P. Puigserver A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis Cell 92 1998 829 839
222. P. Puigserver B.M. Spiegelman Peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1 alpha): Transcriptional coactivator and metabolic regulator Endocrinol. Rev. 24 2003 78 90
223. M. Monsalve Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1 Mol. Cell 6 2000 307 316
224. M.C. Lai B.H. Teh W.Y. Tarn A human papillomavirus E2 transcriptional activator: The interactions with cellular splicing factors and potential function in pre-mRNA processing J. Biol. Chem. 274 1999 11832 11841
225. P. Cramer Coordination between transcription and pre-mRNA processing FEBS Lett. 498 2001 179 182
226. N.A. Faustino T.A. Cooper Pre-mRNA splicing and human disease Genes Dev. 17 2003 419 437
227. M. Vacek P. Sazani R. Kole Antisense-mediated redirection of mRNA splicing Cell. Mol. Life Sci. 60 2003 825 833
228. L. Cartegni A.R. Krainer Correction of disease-associated exon skipping by synthetic exon-specific activators Nat. Struct. Biol. 10 2003 120 125
229. L.A. Skordis M.G. Dunckley B. Yue I.C. Eperon F. Muntoni Bifunctional antisense oligonucleotides provide a trans -acting splicing enhancer that stimulates SMN2 gene expression in patient fibroblasts Proc. Natl. Acad. Sci. USA 100 2003 4114 4119
230. M.J. Simard B. Chabot SRp30c is a repressor of 3′ splice site utilization Mol. Cell. Biol. 22 2002 4001 4010
231. T.O. Tange J. Kjems SF2⧸ASF binds to a splicing enhancer in the third HIV-1 tat exon and stimulates U2AF binding independently of the RS domain J. Mol. Biol. 312 2001 649 662
232. V. Marchand A Janus splicing regulatory element modulates HIV-1 tat and rev mRNA production by coordination of hnRNP A1 cooperative binding J. Mol. Biol. 323 2002 629 652
233. Z.M. Zheng P.J. He C.C. Baker Structural, functional, and protein binding analyses of bovine papillomavirus type 1 exonic splicing enhancers J. Virol. 71 1997 9096 9107
234. W.P. Dirksen X. Li A. Mayeda A.R. Krainer F.M. Rottman Mapping the SF2⧸ASF binding sites in the bovine growth hormone exonic splicing enhancer J. Biol. Chem. 275 2000 29170 29177
235. N. Rooke V. Markovtsov E. Cagavi D.L. Black Roles for SR proteins and hnRNP A1 in the regulation of c-src exon N1 Mol. Cell. Biol. 23 2003 1874 1884
236. M.L. Hastings C.M. Wilson S.H. Munroe A purine-rich intronic element enhances alternative splicing of thyroid hormone receptor mRNA RNA 7 2001 859 874
237. S. Wu C.M. Romfo T.W. Nilsen M.R. Green Functional recognition of the 3′ splice site AG by the splicing factor U2AF35 Nature 402 1999 832 835
238. B. Dauwalder F. Amaya-Manzanares W. Mattox A human homologue of the Drosophila sex determination factor transformer-2 has conserved splicing regulatory functions Proc. Natl. Acad. Sci. USA 93 1996 9004 9009