Xenopus as a model to study alternative splicing in vivo

Biology of the Cell

Volumn 99, Issue 1, 2007, Pages 55-65

  Méreau, Agnes ^a   Le Sommer, Caroline ^a,b   Lerivray, Hubert ^a   Lesimple, Michelle ^a   Hardy, Serge ^a  

^a CNRS   (France)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Development; Embryo; Gene expression; Oocyte; Splicing factor; Xenopus

Indexed keywords

MESSENGER RNA; TRANSCRIPTION FACTOR;

ALTERNATIVE RNA SPLICING; CELL DIFFERENTIATION; CELL FUNCTION; EXON; EXPERIMENTAL MODEL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENETIC MODEL; IN VIVO STUDY; METAMORPHOSIS; NONHUMAN; OOCYTE DEVELOPMENT; OOCYTE MATURATION; ORGANOGENESIS; PRIORITY JOURNAL; REVIEW; RNA SPLICING; XENOPUS;

ALTERNATIVE SPLICING; ANIMALS; EMBRYO, NONMAMMALIAN; MODELS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; TRANS-ACTIVATORS; XENOPUS;

AMPHIBIA; ANIMALIA;

EID: 33846225510     PISSN: 02484900     EISSN: None     Source Type: Journal    
DOI: 10.1042/BC20060073     Document Type: Review

References (73)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F. et al. (2000) The genome sequence of Drosophila melanogaster. Science 287, 2185-2195
2. Allen, B.G. and Weeks, D.L. (2005) Transgenic Xenopus laevis embryos can be generated using phiC31 integrase. Nat. Methods 2, 975-979
3. Audibert, A., Weil, D. and Dautry, F. (2002) In vivo kinetics of mRNA splicing and transport in mammalian cells. Mol. Cell. Biol. 22, 6706-6718
4. Beck, C.W. and Slack, J.M. (1999) Gut specific expression using mammalian promoters in transgenic Xenopus laevis. Mech. Dev. 88, 221-227
5. 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
6. Blanchette, M., Green, R.E., Brenner, S.E. and Rio, D.C. (2005) Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev. 19, 1306-1314
7. Blencowe, B.J. (2000) Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci. 25, 106-110
8. Braddock, M., Thorburn, A.M., Chambers, A., Elliot, G.D., Anderson, G.J., Kingsman, A.J. and Kingsman, S.M. (1990) A nuclear translational block imposed by the HIV-1 U3 region is relieved by the Tat-TAR interaction. Cell 62, 1123-1133
9. Brow, D.A. (2002) Allosteric cascade of spliceosome activation. Annu. Rev. Genet. 36, 333-360
10. Cooper, T.A. (2005) Use of minigene systems to dissect alternative splicing elements. Methods 37, 331-340
11. 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, 11456-11460
12. Davidson, E.H. (1986) Gene activity in early development. Academic Press, New York
13. de Moor, C.H. and Richter, J.D. (2001) Translational control in vertebrate development. Int. Rev. Cytol. 203, 567-608
14. Dumont, J.N. (1972) Oogenesis in Xenopus laevis. J. Morphol. 136, 153-180
15. Duriez, P., Lesimple, M., Allo, M.R. and Hardy, S. (2000) Alternative splicing of Xenopus alphafast-tropomyosin pre-mRNA during development: identification of determining sequences. DNA Cell Biol. 19, 365-376
16. Emmert-Buck, M.R., Bonner, R.F., Smith, P.D., Chuaqui, R.F, Zhuang, Z., Goldstein, S.R., Weiss, R.A. and Liotta, L.A. (1996) Laser capture microdissection. Science 274, 921-922
17. Fink, L. and Bohle, R.M. (2005) Laser microdissection and RNA analysis. Methods Mol. Biol. 293, 167-185
18. Gautier-Courteille, C., Le Clainche, C., Barreau, C., Audic, Y., Graindorge, A., Maniey, D., Osborne, H.B. and Paillard, L. (2004) EDEN-BP-dependent post-transcriptional regulation of gene expression in Xenopus somitic segmentation. Development 131, 6107-6117
19. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F, Hoheisel, J.D., Jacq, C., Johnston, M., Louis, E.J., Mewes, H.W., Murakami, Y., Philippsen, P., Tettelin, H. and Oliver, S.G. (1996) Life with 6000 genes. Science 274, 546-547
20. Golas, M.M., Sander, B., Will, C.L., Luhrmann, R. and Stark, H. (2005) Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy. Mol. Cell 17, 869-883
21. Graindorge, A., Thuret, R., Pollet, N., Osborne, H.B. and Audic, Y. (2006) Identification of post-transcriptionally regulated Xenopus tropicalis maternal mRNAs by microarray. Nucleic Acids Res. 34, 986-995
22. Gurdon, J.B. and Melton, D.A. (1981) Gene transfer in amphibian eggs and oocytes. Annu. Rev. Genet. 15, 189-218
23. Gurdon, J.B. and Wickens, M.P. (1983) The use of Xenopus oocytes for the expression of cloned genes. Methods Enzymol. 101, 370-386
24. Hamm, J., Dathan, N.A. and Mattaj, I.W. (1989) Functional analysis of mutant Xenopus U2 snRNAs. Cell 59, 159-169
25. Hamon, S., Le Sommer, C., Mereau, A., Allo, M.R. and Hardy, S. (2004) Polypyrimidine tract-binding protein is involved in vivo in repression of a composite internal/3′-terminal exon of the Xenopus α-tropomyosin pre-mRNA. J. Biol. Chem. 279, 22166-22175
26. Hartmuth, K., Urlaub, H., Vornlocher, H.P., Will, C.L., Gentzel, M., Wilm, M. and Luhrmann, R. (2002) Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method. Proc. Natl. Acad. Sci. U.S.A. 99, 16719-16724
27. Heasman, J. (2002) Morpholino oligos: making sense of antisense? Dev. Biol. 243, 209-214
28. Heasman, J., Holwill, S. and Wylie, C.C. (1991) Fertilization of cultured Xenopus oocytes and use in studies of maternally inherited molecules. Methods Cell Biol. 36, 213-230
29. Helfman, D.M., Ricci, W.M. and Finn, L.A. (1988) Alternative splicing of tropomyosin pre-mRNAs in vitro and in vivo. Genes Dev. 2, 1627-1638
30. Hernandez, N. and Keller, W. (1983) Splicing of in vitro synthesized messenger RNA precursors in HeLa cell extracts. Cell 35, 89-99
31. Jessus, C. and Ozon, R. (1993) Regulation of cell divisions during oogenesis of vertebrates: the Xenopus oocyte praradigm. Comp. Biochem. Physiol. 106A, 431-448
32. Johnson, A.D. and Krieg, P.A. (1994) pXeX, a vector for efficient expression of cloned sequences in Xenopus embryos. Gene 147, 223-226
33. Johnson, J.M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.D., Santos, R., Schadt, E.E., Stoughton, R. and Shoemaker, D.D. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302, 2141-2144
34. Jonas, E.A., Snape, A.M. and Sargent, T.D. (1989) Transcriptional regulation of a Xenopus embryonic epidermal keratin gene. Development 106, 399-405
35. Jurica, M.S., Licklider, L.J., Gygi, S.R., Grigorieff, N. and Moore, M.J. (2002) Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA 8, 426-439
36. Kenwrick, S., Amaya, E. and Papalopulu, N. (2004) Pilot morpholino screen in Xenopus tropicalis identifies a novel gene involved in head development. Dev. Dyn. 229, 289-299
37. Klinz, F.J. and Gallwitz, D. (1985) Size and position of intervening sequences are critical for the splicing efficiency of pre-mRNA in the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 13, 3791-3804
38. Koide, T., Hayata, T. and Cho, K.W. (2005) Xenopus as a model system to study transcriptional regulatory networks. Proc. Natl. Acad. Sci. U.S.A. 102, 4943-4948
39. Kornblihtt, A.R. (2006) Chromatin, transcript elongation and alternative splicing. Nat. Struct. Mol. Biol. 13, 5-7
40. Kornblihtt, A.R., de la Mata, M., Fededa, J.P., Munoz, M.J. and Nogues, G. (2004) Multiple links between transcription and splicing. RNA 10, 1489-1498
41. Krieg, P.A. and Melton, D.A. (1984) Functional messenger RNAs are produced by SP6 in vitro transcription of cloned cDNAs. Nucleic Acids Res. 12, 7057-7070
42. Kroll, K.L. and Amaya, E. (1996) Transgenic Xenopus embryos from sperm nuclear transplantations reveal FGF signaling requirements during gastrulation. Development 122, 3173-3183
43. Latinkic, B.V., Cooper, B., Smith, S., Kotecha, S., Towers, N., Sparrow, D. and Mohun, T.J. (2004) Transcriptional regulation of the cardiac-specific MLC2 gene during Xenopus embryonic development. Development 131, 669-679
44. Le Sommer, C., Lesimple, M., Mereau, A., Menoret, S., Allo, M.R. and Hardy, S. (2005) PTB regulates the processing of a 3′-terminal exon by repressing both splicing and polyadenylation. Mol. Cell. Biol. 25, 9595-9607
45. Li, M. and Rohrer, B. (2006) Gene silencing in Xenopus laevis by DNA vector-based RNA interference and transgenesis. Cell Res. 16, 99-105
46. Libri, D., Marie, J., Brody, E. and Fiszman, M.Y. (1989) A subfragment of the β-tropomyosin gene is alternatively spliced when transfected into differentiating muscle cells. Nucleic Acids Res. 17, 6449-6462
47. Lim, S.R. and Hertel, K.J. (2004) Commitment to splice site pairing coincides with A complex formation. Mol. Cell 15, 477-483
48. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.-J., Chen, Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380
49. Mayeda, A. and Ohshima, Y. (1988) Short donor site sequences inserted within the intron of β-globin pre-mRNA serve for splicing in vitro. Mol. Cell. Biol. 8, 4484-4491
50. McCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S.D., Wickens, M. and Bentley, D.L. (1997) The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385, 357-361
51. McCullough, A.J. and Berget, S.M. (1997) G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol. Cell. Biol. 17, 4562-4571
52. Milligan, J.F., Groebe, D.R., Witherell, G.W. and Uhlenbeck, O.C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798
53. Modrek, B. and Lee, C. (2002) A genomic view of alternative splicing. Nat. Genet. 30, 13-19
54. Modrek, B. and Lee, C. (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet. 34, 177-180
55. Mohun, T.J., Garrett, N. and Gurdon, J.B. (1986) Upstream sequences required for tissue-specific activation of the cardiac actin gene in Xenopus laevis embryos. EMBO J. 5, 3185-3193
56. Moon, K.H., Zhao, X. and Yu, Y.T. (2006) Pre-mRNA splicing in the nuclei of Xenopus oocytes. Methods Mol. Biol. 322, 149-163
57. Newport, J. and Kirschner, M.W. (1982a) A major developmental transition in early Xenopus embryo: I. Characterization and timing of cellular changes at the midblastula stage. Cell 30, 675-686
58. Newport, J. and Kirschner, M. (1982b) A major developmental transition in early Xenopus embryos: control of the onset of transcription. Cell 30, 687-696
59. Norton, P.A. and Hynes, R.O. (1990) In vitro splicing of fibronectin pre-mRNAs. Nucleic Acids Res. 18, 4089-4097
60. Ogino, H., McConnell, W.B. and Grainger, R.M. (2006) Highly efficient transgenesis in Xenopus tropicalis using I-Scel meganuclease. Mech. Dev. 123, 103-113
61. Paillard, L. and Osborne, H.B. (2003) East of EDEN was a poly(A) tail. Biol. Cell 95, 211-219
62. Pan, Z.Q. and Prives, C. (1989) U2 snRNA sequences that bind U2-specific proteins are dispensable for the function of U2 snRNP in splicing. Genes Dev. 3, 1887-1898
63. Proudfoot, N.J., Furger, A. and Dye, M.J. (2002) Integrating mRNA processing with transcription. Cell 108, 501-512
64. Robberson, B.L., Cote, G.J. and Berget, S.M. (1990) Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10, 84-94
65. Sharp, P.A. (2005) The discovery of split genes and RNA splicing. Trends Biochem. Sci. 30, 279-281
66. Shen, H., Kan, J.L. and Green, M.R. (2004) Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. Mol. Cell. 13, 367-376
67. Signoret, J. and Lefresne, J. (1971) Contribution à l'étude de la segmentation de l'oeuf d'axoloth: I. Definition de la transition blastuléenne. Ann. Emb. Morph. 4, 113-123
68. Sive, H.L., Grainger, R.M. and Harland, R.M. (2000) Early Development of Xenopus laevis: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
69. Smith, C.W. and Valcarcel, J. (2000) Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci. 25, 381-388
70. Smith, L.D., Xu, W. and Varnold, R.L. (1991) Oogenesis and oocyte isolation. Methods Cell Biol. 36, 45-58
71. Sorek, R., Shamir, R. and Ast, G. (2004) How prevalent is functional alternative splicing in the human genome? Trends Genet. 20, 68-71
72. Wu, M. and Gerhart, J. (1991) Raising Xenopus in the laboratory. Methods Cell Biol. 38, 3-17
73. Yu, Y.T., Shu, M.D. and Steitz, J.A. (1998) Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA assembly. EMBO J. 17, 5783-5795