The allele-specific suppressor sup-39 alters use of cryptic splice sites in Caenorhabditis elegans (original) (raw)

Abstract

Mutations in the Caenorhabditis elegans sup-39 gene cause allele-specific suppression of the uncoordination defect of unc-73(e936). e936 is a point mutation that changes the canonical G at the 5' end of intron 16 to a U. This mutation activates three splice donors, two of which define introns beginning with the canonical GU. Use of these two cryptic splice sites causes loss of reading frame; interestingly these messages are not substrates for nonsense-mediated decay. The third splice donor, used in 10% of steady-state e936 messages, is the mutated splice donor at the wild-type position, which defines an intron beginning with UU. In the presence of a sup-39 mutation, these same three splice donors are used, but the ratio of messages produced by splicing at these sites changes. The percentage of unc-73(e936) messages containing the wild-type splice junction is increased to 33% with a corresponding increase in the level of UNC-73 protein. This sup-39-induced change was also observed when the e936 mutant intron region was inserted into a heterologous splicing reporter construct transfected into worms. Experiments with splicing reporter constructs showed that the degree of 5' splice site match to the splicing consensus sequence can strongly influence cryptic splice site choice. We propose that mutant SUP-39 is a new type of informational suppressor that alters the use of weak splice donors.

Full Text

The Full Text of this article is available as a PDF (343.1 KB).

Selected References

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

  1. Ares M., Jr, Weiser B. Rearrangement of snRNA structure during assembly and function of the spliceosome. Prog Nucleic Acid Res Mol Biol. 1995;50:131–159. doi: 10.1016/s0079-6603(08)60813-2. [DOI] [PubMed] [Google Scholar]
  2. Aroian R. V., Levy A. D., Koga M., Ohshima Y., Kramer J. M., Sternberg P. W. Splicing in Caenorhabditis elegans does not require an AG at the 3' splice acceptor site. Mol Cell Biol. 1993 Jan;13(1):626–637. doi: 10.1128/mcb.13.1.626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cáceres J. F., Stamm S., Helfman D. M., Krainer A. R. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science. 1994 Sep 16;265(5179):1706–1709. doi: 10.1126/science.8085156. [DOI] [PubMed] [Google Scholar]
  4. Hodgkin J., Papp A., Pulak R., Ambros V., Anderson P. A new kind of informational suppression in the nematode Caenorhabditis elegans. Genetics. 1989 Oct;123(2):301–313. doi: 10.1093/genetics/123.2.301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Kandels-Lewis S., Séraphin B. Involvement of U6 snRNA in 5' splice site selection. Science. 1993 Dec 24;262(5142):2035–2039. doi: 10.1126/science.8266100. [DOI] [PubMed] [Google Scholar]
  6. Krawczak M., Reiss J., Cooper D. N. The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences. Hum Genet. 1992 Sep-Oct;90(1-2):41–54. doi: 10.1007/BF00210743. [DOI] [PubMed] [Google Scholar]
  7. Lesser C. F., Guthrie C. Mutations in U6 snRNA that alter splice site specificity: implications for the active site. Science. 1993 Dec 24;262(5142):1982–1988. doi: 10.1126/science.8266093. [DOI] [PubMed] [Google Scholar]
  8. Lewis J. A., Fleming J. T. Basic culture methods. Methods Cell Biol. 1995;48:3–29. [PubMed] [Google Scholar]
  9. Li W., Shaw J. E. A variant Tc4 transposable element in the nematode C. elegans could encode a novel protein. Nucleic Acids Res. 1993 Jan 11;21(1):59–67. doi: 10.1093/nar/21.1.59. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lin C. L., Bristol L. A., Jin L., Dykes-Hoberg M., Crawford T., Clawson L., Rothstein J. D. Aberrant RNA processing in a neurodegenerative disease: the cause for absent EAAT2, a glutamate transporter, in amyotrophic lateral sclerosis. Neuron. 1998 Mar;20(3):589–602. doi: 10.1016/s0896-6273(00)80997-6. [DOI] [PubMed] [Google Scholar]
  11. Mello C., Fire A. DNA transformation. Methods Cell Biol. 1995;48:451–482. [PubMed] [Google Scholar]
  12. Newman A., Norman C. Mutations in yeast U5 snRNA alter the specificity of 5' splice-site cleavage. Cell. 1991 Apr 5;65(1):115–123. doi: 10.1016/0092-8674(91)90413-s. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Prelich G. Suppression mechanisms: themes from variations. Trends Genet. 1999 Jul;15(7):261–266. doi: 10.1016/s0168-9525(99)01749-7. [DOI] [PubMed] [Google Scholar]
  15. Pulak R., Anderson P. mRNA surveillance by the Caenorhabditis elegans smg genes. Genes Dev. 1993 Oct;7(10):1885–1897. doi: 10.1101/gad.7.10.1885. [DOI] [PubMed] [Google Scholar]
  16. Rave-Harel N., Kerem E., Nissim-Rafinia M., Madjar I., Goshen R., Augarten A., Rahat A., Hurwitz A., Darvasi A., Kerem B. The molecular basis of partial penetrance of splicing mutations in cystic fibrosis. Am J Hum Genet. 1997 Jan;60(1):87–94. [PMC free article] [PubMed] [Google Scholar]
  17. Run J. Q., Steven R., Hung M. S., van Weeghel R., Culotti J. G., Way J. C. Suppressors of the unc-73 gene of Caenorhabditis elegans. Genetics. 1996 May;143(1):225–236. doi: 10.1093/genetics/143.1.225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Steven R., Kubiseski T. J., Zheng H., Kulkarni S., Mancillas J., Ruiz Morales A., Hogue C. W., Pawson T., Culotti J. UNC-73 activates the Rac GTPase and is required for cell and growth cone migrations in C. elegans. Cell. 1998 Mar 20;92(6):785–795. doi: 10.1016/s0092-8674(00)81406-3. [DOI] [PubMed] [Google Scholar]
  19. Zhang H., Blumenthal T. Functional analysis of an intron 3' splice site in Caenorhabditis elegans. RNA. 1996 Apr;2(4):380–388. [PMC free article] [PubMed] [Google Scholar]