Identification and characterization of RED120: A conserved PWI domain protein with links to splicing and 3′-end formation

FEBS Letters

Volumn 581, Issue 16, 2007, Pages 3087-3097

  Fortes, Puri ^a,d   Longman, Dasa ^b   McCracken, Susan ^c   Ip, Joanna Y ^c   Poot, Raymond ^d   Mattaj, Iain W ^d   Cáceres, Javier F ^b   Blencowe, Benjamin J ^c  

^a UNIVERSITY OF NAVARRA   (Spain)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c UNIVERSITY OF TORONTO   (Canada)

^d EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

3 End processing; RNAi; snRNPs; Splicing; SRm160

Indexed keywords

NUCLEIC ACID BINDING PROTEIN; PROTEIN DERIVATIVE; RED120 PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; HUMAN; HUMAN CELL; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MOTIF; RNA SPLICING;

AMINO ACID SEQUENCE; ANIMALS; ANTIGENS, NUCLEAR; CAENORHABDITIS ELEGANS; CELL NUCLEUS; CLONING, MOLECULAR; CONSERVED SEQUENCE; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEAR MATRIX-ASSOCIATED PROTEINS; PHYLOGENY; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RNA 3' END PROCESSING; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; RNA-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

CAENORHABDITIS ELEGANS;

EID: 34250155674     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.05.066     Document Type: Article

References (55)

1. Jurica M.S., and Moore M.J. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell 12 (2003) 5-14
2. Kramer A. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu. Rev. Biochem. 65 (1996) 367-409
3. Will C.L., and Luhrmann R. Protein functions in pre-mRNA splicing. Curr. Opin. Cell. Biol. 9 (1997) 320-328
4. Blencowe B.J., Bowman A.L., McCracken S., and Rosonina E. SR-related proteins and the processing of messenger RNA precursors. Biochem. Cell Biol. 77 (1999) 277-291
5. Caceres J.F., and Kornblihtt A.R. Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet. 18 (2002) 186-193
6. Fu X.-D. The superfamily of arginine/serine-rich splicing factors. RNA 1 (1995) 663-680
7. Graveley B.R. Sorting out the complexity of SR protein functions. RNA 6 (2000) 1197-1211
8. Maniatis T., and Reed R. An extensive network of coupling among gene expression machines. Nature 416 (2002) 499-506
9. Minvielle-Sebastia L., and Keller W. mRNA polyadenylation and its coupling to other RNA processing reactions and to transcription. Curr. Opin. Cell Biol. 11 (1999) 352-357
10. Gilmartin G.M. Eukaryotic mRNA 3′ processing: a common means to different ends. Genes Dev. 19 (2005) 2517-2521
11. Proudfoot N., and O'Sullivan J. Polyadenylation: a tail of two complexes. Curr. Biol. 12 (2002) R855-R857
12. Kyburz A., Friedlein A., Langen H., and Keller W. Direct interactions between subunits of CPSF and the U2 snRNP contribute to the coupling of pre-mRNA 3′ end processing and splicing. Mol. Cell. 23 (2006) 195-205
13. Millevoi S., Loulergue C., Dettwiler S., Karaa S.Z., Keller W., Antoniou M., and Vagner S. An interaction between U2AF 65 and CF I(m) links the splicing and 3′ end processing machineries. EMBO J. 25 (2006) 4854-4864
14. Vagner S., Vagner C., and Mattaj I.W. The carboxyl terminus of vertebrate poly(A) polymerase interacts with U2AF 65 to couple 3′-end processing and splicing. Genes Dev. 14 (2000) 403-413
15. Hirose Y., and Manley J.L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14 (2000) 1415-1429
16. Tange T.O., Nott A., and Moore M.J. The ever-increasing complexities of the exon junction complex. Curr. Opin. Cell Biol. 16 (2004) 279-284
17. Kataoka N., Yong J., Kim V.N., Velazquez F., Perkinson R.A., Wang F., and Dreyfuss G. Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm. Mol. Cell 6 (2000) 673-682
18. Le Hir H., Izaurralde E., Maquat L.E., and Moore M.J. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19 (2000) 6860-6869
19. Le Hir H., Moore M.J., and Maquat L.E. Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions. Genes Dev. 14 (2000) 1098-1108
20. Kim V.N., Kataoka N., and Dreyfuss G. Role of the nonsense-mediated decay factor hUpf3 in the splicing- dependent exon-exon junction complex. Science 293 (2001) 1832-1836
21. Le Hir H., Gatfield D., Izaurralde E., and Moore M.J. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 20 (2001) 4987-4997
22. Lykke-Andersen J. mRNA quality control: marking the message for life or death. Curr. Biol. 11 (2001) R88-R91
23. Nott A., Le Hir H., and Moore M.J. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev. 18 (2004) 210-222
24. Tange T.O., Shibuya T., Jurica M.S., and Moore M.J. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 11 (2005) 1869-1883
25. Blencowe B.J., Issner R., Nickerson J.A., and Sharp P.A. A coactivator of pre-mRNA splicing. Genes Dev. 12 (1998) 996-1009
26. Eldridge A.G., Li Y., Sharp P.A., and Blencowe B.J. The SRm160/300 splicing coactivator is required for exon-enhancer function. Proc. Natl. Acad. Sci. USA 96 (1999) 6125-6130
27. McCracken S., Lambermon M., and Blencowe B.J. SRm160 splicing coactivator promotes transcript 3′-end cleavage. Mol. Cell Biol. 22 (2002) 148-160
28. Szymczyna B.R., et al. Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing. Genes Dev. 17 (2003) 461-475
29. Blencowe B.J., Nickerson J.A., Issner R., Penman S., and Sharp P.A. Association of nuclear matrix antigens with exon-containing splicing complexes. J. Cell Biol. 127 (1994) 593-607
30. Wan K., Nickerson J.A., Krockmalnic G., and Penman S. The B1C8 protein is in the dense assemblies of the nuclear matrix and relocates to the spindle and pericentriolar filaments at mitosis. Proc. Natl. Acad. Sci. USA 91 (1994) 594-598
31. Blencowe B.J., Bauren G., Eldridge A.G., Issner R., Nickerson J.A., Rosonina E., and Sharp P.A. The SRm160/300 splicing coactivator subunits. RNA 6 (2000) 111-120
32. Fabrizio P., Laggerbauer B., Lauber J., Lane W.S., and Luhrmann R. An evolutionarily conserved U5 snRNP-specific protein is a GTP-binding factor closely related to the ribosomal translocase EF-2. EMBO J. 16 (1997) 4092-4106
33. Izaurralde E., Lewis J., McGuigan C., Jankowska M., Darzynkiewicz E., and Mattaj I.W. A nuclear cap binding protein complex involved in pre-mRNA splicing. Cell 78 (1994) 657-668
34. Trembley J.H., Hu D., Hsu L.C., Yeung C.Y., Slaughter C., Lahti J.M., and Kidd V.J. PITSLRE p110 protein kinases associate with transcription complexes and affect their activity. J. Biol. Chem. 277 (2002) 2589-2596
35. Gatfield D., and Izaurralde E. REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export. J. Cell Biol. 159 (2002) 579-588
36. Lerner E.A., Lerner M.R., Janeway Jr. C.A., and Steitz J.A. Monoclonal antibodies to nucleic acid-containing cellular constituents: probes for molecular biology and autoimmune disease. Proc. Natl. Acad. Sci. USA 78 (1981) 2737-2741
37. Fu X.D., and Maniatis T. Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343 (1990) 437-441
38. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
39. Blencowe B.J., and Ouzounis C.A. The PWI motif: a new protein domain in splicing factors. Trends Biochem. Sci. 24 (1999) 179-180
40. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., and Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res. 30 (2002) 235-238
41. Wootton J.C., and Federhen S. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266 (1996) 554-571
42. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
43. Fortes P., Lamond A.I., and Ortin J. Influenza virus NS1 protein alters the subnuclear localization of cellular splicing components. J. Gen. Virol. 76 Pt 4 (1995) 1001-1107
44. Dignam J.D., Lebovitz R.M., and Roeder R.G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11 (1983) 1475-1489
45. Fortes P., Bilbao-Cortes D., Fornerod M., Rigaut G., Raymond W., Seraphin B., and Mattaj I.W. Luc7p, a novel yeast U1 snRNP protein with a role in 5′ splice site recognition. Genes Dev. 13 (1999) 2425-2438
46. Hamm J., Dathan N.A., and Mattaj I.W. Functional analysis of mutant Xenopus U2 snRNAs. Cell 59 (1989) 159-169
47. Longman D., Johnstone I.L., and Caceres J.F. The Ref/Aly proteins are dispensable for mRNA export and development in Caenorhabditis elegans. RNA 9 (2003) 881-891
48. Longman D., McGarvey T., McCracken S., Johnstone I.L., Blencowe B.J., and Caceres J.F. Multiple interactions between SRm160 and SR family proteins in enhancer-dependent splicing and development of C. elegans. Curr. Biol. 11 (2001) 1923-1933
49. McCracken S., et al. Proteomic analysis of SRm160-containing complexes reveals a conserved association with cohesin. J. Biol. Chem. 280 (2005) 42227-42236
50. Sherrington R., et al. Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease. Nature 375 (1995) 754-760
51. Gottschalk A., et al. A comprehensive biochemical and genetic analysis of the yeast U1 snRNP reveals five novel proteins. RNA 4 (1998) 374-393
52. Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., and Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17 (1999) 1030-1032
53. Fortes P., Kufel J., Fornerod M., Polycarpou-Schwarz M., Lafontaine D., Tollervey D., and Mattaj I.W. Genetic and physical interactions involving the yeast nuclear cap-binding complex. Mol. Cell Biol. 19 (1999) 6543-6553
54. McCracken S., Longman D., Johnstone I.L., Caceres J.F., and Blencowe B.J. An evolutionarily conserved role for SRm160 in 3′-end processing that functions independently of exon junction complex formation. J. Biol. Chem. 278 (2003) 44153-44160
55. Zhou Z., Licklider L.J., Gygi S.P., and Reed R. Comprehensive proteomic analysis of the human spliceosome. Nature 419 (2002) 182-185