Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila

Genes and Development

Volumn 19, Issue 11, 2005, Pages 1306-1314

  Blanchette, Marco ^a   Green, Richard E ^a,b   Brenner, Steven E ^a,b   Rio, Donald C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alternative splicing; Drosophila melanogaster; hnRNP proteins; Microarray; SR proteins

Indexed keywords

MESSENGER RNA; PROTEIN SUBUNIT; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; DROSOPHILA; GENE SEQUENCE; GENOME ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA SPLICING;

ANIMALS; BINDING SITES; DROSOPHILA MELANOGASTER; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER;

DROSOPHILA MELANOGASTER;

EID: 22344458119     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.1314205     Document Type: Article

References (45)

1. Amarasinghe, A.K., MacDiarmid, R., Adams, M.D., and Rio, D.C. 2001. An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element. RNA 7: 1239-1253.
2. Black, D.L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72: 291-336
3. Brett, D., Pospisil, H., Valcarcel, J., Reich, J., and Bork, P. 2002. Alternative splicing and genome complexity. Nat. Genet. 30: 29-30.
4. Burckin, T., Nagel, R., Mandel-Gutfreund, Y., Shiue, L., Clark, T.A., Chong, J.L., Chang, T.H., Squazzo, S., Hartzog, G., and Ares Jr., M. 2005. Exploring functional relationships between components of the gene expression machinery. Nat. Struct. Mol. Biol. 12: 175-182.
5. Burnette, J.M., Hatton, A.R., and Lopez, A.J. 1999. Trans-acting factors required for inclusion of regulated exons in the Ultrabithorax mRNAs of Drosophila melanogaster. Genetics 151: 1517-1529.
6. Cáceres, J.F., Stamm, S., Helfman, D.M., and Krainer, A.R. 1994. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science 265: 1706-1709.
7. Caputi, M. and Zahler, A.M. 2002. SR proteins and hnRNP H regulate the splicing of the HIV-1 tev-specific exon 6D. EMBO J. 21: 845-855.
8. Caputi, M., Mayeda, A., Krainer, A.R., and Zahler, A.M. 1999. hnRNP A/B proteins are required for inhibition of HIV-1 pre-mRNA splicing. EMBO J. 18: 4060-4067.
9. Castle, J., Garrett-Engele, P., Armour, C.D., Duenwald, S.J., Loerch, P.M., Meyer, M.R., Schadt, E.E., Stoughton, R., Parrish, M.L., Shoemaker, D.D., et al. 2003. Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol. 4: R66.
10. Celniker, S.E. and Rubin, G.M. 2003. The Drosophila melanogaster genome. Annu. Rev. Genomics Hum. Genet. 4: 89-117.
11. Clark, T.A., Sugnet, C.W., and Ares Jr., M. 2002. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296: 907-910.
12. Clemens, J.C., Worby, C.A., Simonson-Leff, N., Muda, M., Maehama, T., Hemmings, B.A., and Dixon, J.E. 2000. Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc. Natl. Acad. Sci. 97: 6499-6503.
13. Coulter, L.R., Landree, M.A., and Cooper, T.A. 1997. Identification of a new class of exonic splicing enhancers by in vivo selection Mol. Cell Biol. 17: 2143-2150. [Published erratum appears in Mol. Cell Biol. 1997. 17: 3468].
14. Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868.
15. 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. 89: 11224-11228.
16. Hu, G.K., Madore, S.J., Moldover, B., Jatkoe, T., Balaban, D., Thomas, J., and Wang, Y. 2001. Predicting splice variant from DNA chip expression data. Genome Res. 11:1237-1245.
17. Jacquenet, S., Mereau, A., Bilodeau, P.S., Damier, L., Stoltzfus, C.M., and Branlant, C. 2001. A second exon splicing silencer within human immunodeficiency virus type 1 tat exon 2 represses splicing of Tat mRNA and binds protein hnRNP H. J. Biol. Chem. 276: 40464-40475.
18. 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.
19. Jurica, M.S. and Moore, M.J. 2003. Pre-mRNA splicing: Awash in a sea of proteins. Mol. Cell 12: 5-14.
20. Kim, S., Shi, H., Lee, D.K., and Lis, J.T. 2003. Specific SR protein-dependent splicing substrates identified through genomic SELEX. Nucleic Acids Res. 31: 1955-1961.
21. Labourier, E., Blanchette, M., Feiger, J.W., Adams, M.D., and Rio, D.C. 2002. The KH-type RNA-binding protein PSI is required for Drosophila viability, male fertility, and cellular mRNA processing. Genes & Dev. 16: 72-84.
22. Lee, C. and Roy, M. 2004. Analysis of alternative splicing with microarrays: Successes and challenges. Genome Biol. 5: 231.
23. Liu, H.X., Zhang, M., and Krainer, A.R. 1998. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes & Dev. 12: 1998-2012.
24. 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.
25. Lynch, K.W. and Maniatis, T. 1996. Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer. Genes & Dev. 10: 2089-2101.
26. Maniatis, T. and Tasic, B. 2002. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418: 236-243.
27. Mayeda, A. and Krainer, A.R. 1992. Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell 68: 365-375.
28. Moore, M.J., Query, C.C., and Sharp, P.A. 1993. Splicing of precursors to messenger RNAs by the spliceosome. In The RNA world (eds. R.F. Gesteland and J.F. Atkins), pp. 303-357. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
29. Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A.L., Mohammad, N., Babak, T., Siu, H., Hughes, T.R., Morris, Q.D., et al. 2004. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell 16: 929-941.
30. Relogio, A., Ben-Dov, C., Baum, M., Ruggiu, M., Gemund, C., Benes, V., Darnell, R.B., and Valcarcel, J. 2005. Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. J. Biol. Chem. 280: 4779-4784.
31. Shi, H., Hoffman, B.E., and Lis, J.T. 1997. A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52. Mol. Cell. Biol. 17: 2649-2657.
32. Siebel, C.W., Fresco, L.D., and Rio, D.C. 1992. The mechanism of somatic inhibition of Drosophila P-element pre-mRNA splicing: Multiprotein complexes at an exon pseudo-5′ splice site control U1 snRNP binding. Genes & Dev. 6: 1386-1401.
33. Siebel, C.W., Kanaar, R., and Rio, D.C. 1994. Regulation of tissue-specific P-element pre-mRNA splicing requires the RNA-binding protein PSI. Genes & Dev. 8: 1713-1725.
34. Siebel, C.W., Admon, A., and Rio, D.C. 1995. Soma-specific expression and cloning of PSI, a negative regulator of P element pre-mRNA splicing. Genes & Dev. 9: 269-283.
35. Smith, C.W. and Valcarcel, J. 2000. Alternative pre-mRNA splicing: The logic of combinatorial control. Trends Biochem. Sci. 25: 381-388.
36. Stolc, V., Gauhar, Z., Mason, C., Halasz, G., van Batenburg, M.F., Rifkin, S.A., Hua, S., Herreman, T., Tongprasit, W., Barbano, P.E., et al. 2004. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306: 655-660.
37. Tacke, R. and Manley, J.L. 1995. The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J. 14: 3540-3551.
38. Wang, J., Takagaki, Y., and Manley, J.L. 1996. Targeted disruption of an essential vertebrate gene: ASF/SF2 is required for cell viability. Genes & Dev. 10: 2588-2599.
39. Wang, J., Xiao, S.H., and Manley, J.L. 1998. Genetic analysis of the SR protein ASF/SF2: Interchangeability of RS domains and negative control of splicing. Genes & Dev. 12: 2222-2233.
40. Wang, H., Hubbell, E., Hu, J.S., Mei, G., Cline, M., Lu, G., Clark, T., Siani-Rose, M.A., Ares, M., Kulp, D.C., et al. 2003. Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics 19 (Suppl. 1): i315-i322.
41. Wang, Z., Rolish, M.E., Yeo, G., Tung, V., Mawson, M., and Burge, C.B. 2004. Systematic identification and analysis of exonic splicing silencers. Cell 119: 831-845.
42. Wheelan, S.J., Church, D.M., and Ostell, J.M. 2001. Spidey: A tool for mRNA-to-genomic alignments. Genome Res. 11:1952-1957.
43. 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.
44. Zahler, A.M., Damgaard, C.K., Kjems, J., and Caputi, M. 2004. SC35 and heterogeneous nuclear ribonucleoprotein A/B proteins bind to a juxtaposed exonic splicing enhancer/exonic splicing silencer element to regulate HIV-1 tat exon 2 splicing. J. Biol. Chem. 279: 10077-10084.
45. Zhu, J., Mayeda, A., and Krainer, A.R. 2001. Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. Mol. Cell 8: 1351-1361.