Co-regulation of alternative splicing by diverse splicing factors in Caenorhabditis elegans

Nucleic Acids Research

Volumn 39, Issue 2, 2011, Pages 666-674

  Barberan Soler, Sergio ^a   Medina, Pedro ^a   Estella, Jeffrey ^a   Williams, James ^a   Zahler, Alan M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; SPLICING FACTOR; UNCLASSIFIED DRUG;

ALLELE; ALTERNATIVE RNA SPLICING; ARTICLE; CAENORHABDITIS ELEGANS; DEVELOPMENT; DNA MICROARRAY; EXON; GENE DELETION; GENETIC STRAIN; MISSENSE MUTATION; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; WILD TYPE;

ALTERNATIVE SPLICING; ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA-BINDING PROTEINS;

CAENORHABDITIS ELEGANS;

EID: 79551494105     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq767     Document Type: Article

References (40)

1. Martinez-Contreras, R., Cloutier, P., Shkreta, L., Fisette, J.F., Revil, T. and Chabot, B. (2007) hnRNP proteins and splicing control. Adv. Exp. Med. Biol., 623, 123-147.
2. Lin, S. and Fu, X.D. (2007) SR proteins and related factors in alternative splicing. Adv. Exp. Med. Biol., 623, 107-122.
3. Kanopka, A., Muhlemann, O. and Akusjarvi, G. (1996) Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA. Nature, 381, 535-538.
4. Martinez-Contreras, R., Fisette, J.F., Nasim, F.U., Madden, R., Cordeau, M. and Chabot, B. (2006) Intronic binding sites for hnRNP A/B and hnRNP F/H proteins stimulate pre-mRNA splicing. PLoS Biol, 4, e21.
5. Ben-Dov, C., Hartmann, B., Lundgren, J. and Valcarcel, J. (2008) Genome-wide analysis of alternative pre-mRNA splicing. J. Biol. Chem., 283, 1229-1233.
6. Wang, Z. and Burge, C.B. (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA, 14, 802-813.
7. Nilsen, T.W. and Graveley, B.R. (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature, 463, 457-463.
8. Barash, Y., Calarco, J.A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B.J. and Frey, B.J. Deciphering the splicing code. Nature, 465, 53-59.
9. David, C.J., Chen, M., Assanah, M., Canoll, P. and Manley, J.L. (2010) HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer. Nature, 463, 364-368.
10. Clower, C.V., Chatterjee, D., Wang, Z., Cantley, L.C., Vander Heiden, M.G. and Krainer, A.R. (2010) The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism. Proc. Natl Acad. Sci. USA, 107, 1894-1899.
11. Fisette, J.F., Toutant, J., Dugre-Brisson, S., Desgroseillers, L. and Chabot, B. hnRNP A1 and hnRNP H can collaborate to modulate 5' splice site selection. RNA, 16, 228-238.
12. Underwood, J.G., Boutz, P.L., Dougherty, J.D., Stoilov, P. and Black, D.L. (2005) Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Mol. Cell. Biol., 25, 10005-10016.
13. Venables, J.P., Koh, C.S., Froehlich, U., Lapointe, E., Couture, S., Inkel, L., Bramard, A., Paquet, E.R., Watier, V., Durand, M. et al. (2008) Multiple and specific mRNA processing targets for the major human hnRNP proteins. Mol. Cell. Biol., 28, 6033-6043.
14. Blanchette, M., Green, R.E., MacArthur, S., Brooks, A.N., Brenner, S.E., Eisen, M.B. and Rio, D.C. (2009) Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol. Cell, 33, 438-449.
15. Motta-Mena, L.B., Heyd, F. and Lynch, K.W. Context-dependent regulatory mechanism of the splicing factor hnRNP L. Mol. Cell, 37, 223-234.
16. Zahler, A.M. (2005) Alternative splicing in C. elegans. In The C. elegans Research Community (ed.), WormBook, doi/10.1895/ wormbook1.31.1, http://www.wormbook.org.
17. Kuroyanagi, H., Kobayashi, T., Mitani, S. and Hagiwara, M. (2006) Transgenic alternative-splicing reporters reveal tissue-specific expression profiles and regulation mechanisms in vivo. Nat. Methods, 3, 909-915.
18. Kuroyanagi, H., Ohno, G., Mitani, S. and Hagiwara, M. (2007) The Fox-1 family and SUP-12 coordinately regulate tissue-specific alternative splicing in vivo. Mol. Cell. Biol., 27, 8612-8621.
19. Ohno, G., Hagiwara, M. and Kuroyanagi, H. (2008) STAR family RNA-binding protein ASD-2 regulates developmental switching of mutually exclusive alternative splicing in vivo. Genes Dev., 22, 360-374.
20. Spike, C.A., Davies, A.G., Shaw, J.E. and Herman, R.K. (2002) MEC-8 regulates alternative splicing of unc-52 transcripts in C. elegans hypodermal cells. Development, 129, 4999-5008.
21. Spartz, A.K., Herman, R.K. and Shaw, J.E. (2004) SMU-2 and SMU-1, Caenorhabditis elegans homologs of mammalian spliceosome-associated proteins RED and fSAP57, work together to affect splice site choice. Mol. Cell. Biol., 24, 6811-6823.
22. Davies, A.G., Spike, C.A., Shaw, J.E. and Herman, R.K. (1999) Functional overlap between the mec-8 gene and five sym genes in Caenorhabditis elegans. Genetics, 153, 117-134.
23. Barberan-Soler, S., Lambert, N.J. and Zahler, A.M. (2009) Global analysis of alternative splicing uncovers developmental regulation of nonsense-mediated decay in C. elegans. RNA, 15, 1652-1660.
24. Barberan-Soler, S. and Zahler, A.M. (2008) Alternative splicing and the steady-state ratios of mRNA isoforms generated by it are under strong stabilizing selection in Caenorhabditis elegans. Mol. Biol. Evol., 25, 2431-2437.
25. Barberan-Soler, S. and Zahler, A.M. (2008) Alternative splicing regulation during C. elegans development: splicing factors as regulated targets. PLoS Genet., 4, e1000001.
26. Chalfie, M. and Sulston, J. (1981) Developmental genetics of the mechanosensory neurons of Caenorhabditis elegans. Dev. Biol., 82, 358-370.
27. Skipper, M., Milne, C.A. and Hodgkin, J. (1999) Genetic and molecular analysis of fox-1, a numerator element involved in Caenorhabditis elegans primary sex determination. Genetics, 151, 617-631.
28. Anderson, P. and Brenner, S. (1984) A selection for myosin heavy chain mutants in the nematode Caenorhabditis elegans. Proc. Natl Acad. Sci. USA, 81, 4470-4474.
29. Francis, G.R. and Waterston, R.H. (1985) Muscle organization in Caenorhabditis elegans: localization of proteins implicated in thin filament attachment and I-band organization. J. Cell. Biol., 101, 1532-1549.
30. Pfaffl, M.W. (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res., 29, e45.
31. Anyanful, A., Ono, K., Johnsen, R.C., Ly, H., Jensen, V., Baillie, D.L. and Ono, S. (2004) The RNA-binding protein SUP-12 controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. J. Cell. Biol., 167, 639-647.
32. Longman D., Johnstone, I.L. and Caceres, J.F. (2000) Functional characterization of SR and SR-related genes in Caenorhabditis elegans. EMBO J. 19, 1625-1637.
33. Loria, P.M., Duke, A., Rand, J.B. and Hobert, O. (2003) Two neuronal, nuclear-localized RNA binding proteins involved in synaptic transmission. Curr. Biol., 13, 1317-1323.
34. Lundquist, E.A. and Herman, R.K. (1994) The mec-8 gene of Caenorhabditis elegans affects muscle and sensory neuron function and interacts with three other genes: unc-52, smu-1 and smu-2. Genetics, 138, 83-101.
35. Kawano, T., Fujita, M. and Sakamoto, H. (2000) Unique and redundant functions of SR proteins, a conserved family of splicing factors, in Caenorhabditis elegans development. Mech. Dev., 95, 67-76.
36. The Universal Protein Resource. (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
37. Tian, M. and Maniatis, T. (1992) Positive control of pre-mRNA splicing in vitro. Science, 256, 237-240.
38. Rooke, N., Markovtsov, V., Cagavi, E. and Black, D.L. (2003) Roles for SR proteins and hnRNP A1 in the regulation of c-src exon N1. Mol. Cell. Biol., 23, 1874-1884.
39. Lundquist, E.A., Herman, R.K., Rogalski, T.M., Mullen, G.P., Moerman, D.G. and Shaw, J.E. (1996) The mec-8 gene of C. elegans encodes a protein with two RNA recognition motifs and regulates alternative splicing of unc-52 transcripts. Development, 122, 1601-1610.
40. Yochem, J., Bell, L.R. and Herman, R.K. (2004) The identities of sym-2, sym-3 and sym-4, three genes that are synthetically lethal with mec-8 in Caenorhabditis elegans. Genetics, 168, 1293-1306.