Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 1999 Apr;151(4):1517–1529. doi: 10.1093/genetics/151.4.1517

Trans-acting factors required for inclusion of regulated exons in the Ultrabithorax mRNAs of Drosophila melanogaster.

J M Burnette 1, A R Hatton 1, A J Lopez 1
PMCID: PMC1460545  PMID: 10101174

Abstract

Alternatively spliced Ultrabithorax mRNAs differ by the presence of internal exons mI and mII. Two approaches were used to identify trans-acting factors required for inclusion of these cassette exons. First, mutations in a set of genes implicated in the control of other alternative splicing decisions were tested for dominant effects on the Ubx alternative splicing pattern. To identify additional genes involved in regulation of Ubx splicing, a large collection of deficiencies was tested first for dominant enhancement of the haploinsufficient Ubx haltere phenotype and second for effects on the splicing pattern. Inclusion of the cassette exons in Ubx mRNAs was reduced strongly in heterozygotes for hypomorphic alleles of hrp48, which encodes a member of the hnRNP A/B family and is implicated in control of P-element splicing. Significant reductions of mI and mII inclusion were also observed in heterozygotes for loss-of-function alleles of virilizer, fl(2)d, and crooked neck. The products of virilizer and fl(2)d are also required for Sxl autoregulation at the level of splicing; crooked neck encodes a protein with structural similarities to yeast-splicing factors Prp39p and Prp42p. Deletion of at least five other loci caused significant reductions in the inclusion of mI and/or mII. Possible roles of identified factors are discussed in the context of the resplicing strategy for generation of alternative Ubx mRNAs.

Full Text

The Full Text of this article is available as a PDF (236.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams M. D., Tarng R. S., Rio D. C. The alternative splicing factor PSI regulates P-element third intron splicing in vivo. Genes Dev. 1997 Jan 1;11(1):129–138. doi: 10.1101/gad.11.1.129. [DOI] [PubMed] [Google Scholar]
  2. Berget S. M. Exon recognition in vertebrate splicing. J Biol Chem. 1995 Feb 10;270(6):2411–2414. doi: 10.1074/jbc.270.6.2411. [DOI] [PubMed] [Google Scholar]
  3. Black D. L. Finding splice sites within a wilderness of RNA. RNA. 1995 Oct;1(8):763–771. [PMC free article] [PubMed] [Google Scholar]
  4. Bomze H. M., López A. J. Evolutionary conservation of the structure and expression of alternatively spliced Ultrabithorax isoforms from Drosophila. Genetics. 1994 Mar;136(3):965–977. doi: 10.1093/genetics/136.3.965. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chabot B. Directing alternative splicing: cast and scenarios. Trends Genet. 1996 Nov;12(11):472–478. doi: 10.1016/0168-9525(96)10037-8. [DOI] [PubMed] [Google Scholar]
  6. Champlin D. T., Frasch M., Saumweber H., Lis J. T. Characterization of a Drosophila protein associated with boundaries of transcriptionally active chromatin. Genes Dev. 1991 Sep;5(9):1611–1621. doi: 10.1101/gad.5.9.1611. [DOI] [PubMed] [Google Scholar]
  7. Cline T. W., Meyer B. J. Vive la différence: males vs females in flies vs worms. Annu Rev Genet. 1996;30:637–702. doi: 10.1146/annurev.genet.30.1.637. [DOI] [PubMed] [Google Scholar]
  8. Cooper T. A., Mattox W. The regulation of splice-site selection, and its role in human disease. Am J Hum Genet. 1997 Aug;61(2):259–266. doi: 10.1086/514856. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Deshpande G., Samuels M. E., Schedl P. D. Sex-lethal interacts with splicing factors in vitro and in vivo. Mol Cell Biol. 1996 Sep;16(9):5036–5047. doi: 10.1128/mcb.16.9.5036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fu X. D. The superfamily of arginine/serine-rich splicing factors. RNA. 1995 Sep;1(7):663–680. [PMC free article] [PubMed] [Google Scholar]
  11. Grabowski P. J. Splicing regulation in neurons: tinkering with cell-specific control. Cell. 1998 Mar 20;92(6):709–712. doi: 10.1016/s0092-8674(00)81399-9. [DOI] [PubMed] [Google Scholar]
  12. Granadino B., Penalva L. O., Sánchez L. The gene fl(2)d is needed for the sex-specific splicing of transformer pre-mRNA but not for double-sex pre-mRNA in Drosophila melanogaster. Mol Gen Genet. 1996 Nov 27;253(1-2):26–31. doi: 10.1007/s004380050292. [DOI] [PubMed] [Google Scholar]
  13. Granadino B., San Juán A., Santamaria P., Sánchez L. Evidence of a dual function in fl(2)d, a gene needed for Sex-lethal expression in Drosophila melanogaster. Genetics. 1992 Mar;130(3):597–612. doi: 10.1093/genetics/130.3.597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hammond L. E., Rudner D. Z., Kanaar R., Rio D. C. Mutations in the hrp48 gene, which encodes a Drosophila heterogeneous nuclear ribonucleoprotein particle protein, cause lethality and developmental defects and affect P-element third-intron splicing in vivo. Mol Cell Biol. 1997 Dec;17(12):7260–7267. doi: 10.1128/mcb.17.12.7260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hatton A. R., Subramaniam V., Lopez A. J. Generation of alternative Ultrabithorax isoforms and stepwise removal of a large intron by resplicing at exon-exon junctions. Mol Cell. 1998 Dec;2(6):787–796. doi: 10.1016/s1097-2765(00)80293-2. [DOI] [PubMed] [Google Scholar]
  16. Haynes S. R., Cooper M. T., Pype S., Stolow D. T. Involvement of a tissue-specific RNA recognition motif protein in Drosophila spermatogenesis. Mol Cell Biol. 1997 May;17(5):2708–2715. doi: 10.1128/mcb.17.5.2708. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Haynes S. R., Johnson D., Raychaudhuri G., Beyer A. L. The Drosophila Hrb87F gene encodes a new member of the A and B hnRNP protein group. Nucleic Acids Res. 1991 Jan 11;19(1):25–31. doi: 10.1093/nar/19.1.25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Heinrichs V., Baker B. S. The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences. EMBO J. 1995 Aug 15;14(16):3987–4000. doi: 10.1002/j.1460-2075.1995.tb00070.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hilfiker A., Amrein H., Dübendorfer A., Schneiter R., Nöthiger R. The gene virilizer is required for female-specific splicing controlled by Sxl, the master gene for sexual development in Drosophila. Development. 1995 Dec;121(12):4017–4026. doi: 10.1242/dev.121.12.4017. [DOI] [PubMed] [Google Scholar]
  20. Kornfeld K., Saint R. B., Beachy P. A., Harte P. J., Peattie D. A., Hogness D. S. Structure and expression of a family of Ultrabithorax mRNAs generated by alternative splicing and polyadenylation in Drosophila. Genes Dev. 1989 Feb;3(2):243–258. doi: 10.1101/gad.3.2.243. [DOI] [PubMed] [Google Scholar]
  21. Krämer A. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu Rev Biochem. 1996;65:367–409. doi: 10.1146/annurev.bi.65.070196.002055. [DOI] [PubMed] [Google Scholar]
  22. Lopez A. J. Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu Rev Genet. 1998;32:279–305. doi: 10.1146/annurev.genet.32.1.279. [DOI] [PubMed] [Google Scholar]
  23. Lopez A. J., Hogness D. S. Immunochemical dissection of the Ultrabithorax homeoprotein family in Drosophila melanogaster. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):9924–9928. doi: 10.1073/pnas.88.22.9924. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lynch K. W., Maniatis T. Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer. Genes Dev. 1996 Aug 15;10(16):2089–2101. doi: 10.1101/gad.10.16.2089. [DOI] [PubMed] [Google Scholar]
  25. MacDougall C., Harbison D., Bownes M. The developmental consequences of alternate splicing in sex determination and differentiation in Drosophila. Dev Biol. 1995 Dec;172(2):353–376. doi: 10.1006/dbio.1995.8047. [DOI] [PubMed] [Google Scholar]
  26. Matunis E. L., Matunis M. J., Dreyfuss G. Characterization of the major hnRNP proteins from Drosophila melanogaster. J Cell Biol. 1992 Jan;116(2):257–269. doi: 10.1083/jcb.116.2.257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. McLean M. R., Rymond B. C. Yeast pre-mRNA splicing requires a pair of U1 snRNP-associated tetratricopeptide repeat proteins. Mol Cell Biol. 1998 Jan;18(1):353–360. doi: 10.1128/mcb.18.1.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. O'Connor M. B., Binari R., Perkins L. A., Bender W. Alternative RNA products from the Ultrabithorax domain of the bithorax complex. EMBO J. 1988 Feb;7(2):435–445. doi: 10.1002/j.1460-2075.1988.tb02831.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Peng X., Mount S. M. Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor. Mol Cell Biol. 1995 Nov;15(11):6273–6282. doi: 10.1128/mcb.15.11.6273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ring H. Z., Lis J. T. The SR protein B52/SRp55 is essential for Drosophila development. Mol Cell Biol. 1994 Nov;14(11):7499–7506. doi: 10.1128/mcb.14.11.7499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Roth M. B., Zahler A. M., Stolk J. A. A conserved family of nuclear phosphoproteins localized to sites of polymerase II transcription. J Cell Biol. 1991 Nov;115(3):587–596. doi: 10.1083/jcb.115.3.587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Salz H. K., Flickinger T. W. Both loss-of-function and gain-of-function mutations in snf define a role for snRNP proteins in regulating Sex-lethal pre-mRNA splicing in Drosophila development. Genetics. 1996 Sep;144(1):95–108. doi: 10.1093/genetics/144.1.95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Samuels M., Deshpande G., Schedl P. Activities of the Sex-lethal protein in RNA binding and protein:protein interactions. Nucleic Acids Res. 1998 Jun 1;26(11):2625–2637. doi: 10.1093/nar/26.11.2625. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Schwer B., Guthrie C. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature. 1991 Feb 7;349(6309):494–499. doi: 10.1038/349494a0. [DOI] [PubMed] [Google Scholar]
  35. Siebel C. W., Admon A., Rio D. C. Soma-specific expression and cloning of PSI, a negative regulator of P element pre-mRNA splicing. Genes Dev. 1995 Feb 1;9(3):269–283. doi: 10.1101/gad.9.3.269. [DOI] [PubMed] [Google Scholar]
  36. Siebel C. W., Kanaar R., Rio D. C. Regulation of tissue-specific P-element pre-mRNA splicing requires the RNA-binding protein PSI. Genes Dev. 1994 Jul 15;8(14):1713–1725. doi: 10.1101/gad.8.14.1713. [DOI] [PubMed] [Google Scholar]
  37. Tirronen M., Roos C. The kurz locus of Drosophila melanogaster shares conserved motifs with a family of yeast ATP dependent splicing factors. Nucleic Acids Res. 1992 Apr 11;20(7):1802–1802. doi: 10.1093/nar/20.7.1802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Wang J., Manley J. L. Regulation of pre-mRNA splicing in metazoa. Curr Opin Genet Dev. 1997 Apr;7(2):205–211. doi: 10.1016/s0959-437x(97)80130-x. [DOI] [PubMed] [Google Scholar]
  39. Wu J. Y., Maniatis T. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell. 1993 Dec 17;75(6):1061–1070. doi: 10.1016/0092-8674(93)90316-i. [DOI] [PubMed] [Google Scholar]
  40. Zhang K., Smouse D., Perrimon N. The crooked neck gene of Drosophila contains a motif found in a family of yeast cell cycle genes. Genes Dev. 1991 Jun;5(6):1080–1091. doi: 10.1101/gad.5.6.1080. [DOI] [PubMed] [Google Scholar]
  41. zur Lage P., Shrimpton A. D., Flavell A. J., Mackay T. F., Brown A. J. Genetic and molecular analysis of smooth, a quantitative trait locus affecting bristle number in Drosophila melanogaster. Genetics. 1997 Jun;146(2):607–618. doi: 10.1093/genetics/146.2.607. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES