Abstract
In eukaryotic cells, double-stranded RNA is degraded to 21mers and triggers RNA interference. Using a pattern description language, we have searched the EMBL database for sequences with the potential to form double strands in cis in Dictyostelium discoideum. No extended inverted repeats were found in mRNAs. However, the antisense direction of some mRNAs encoding regulatory or developmentally regulated proteins showed the ability to form double-stranded regions. In EST archives, we found potential double strands derived from a few genes, but these transcripts are not continuously encoded in the genome. Most likely, they represent hybrid molecules of sense and antisense RNAs.
References
Bartsch, H., Voigtsberger, S., Baumann, G., Morano, I., and Luther, H. P. (2004). Detection of a novel sense-antisense RNA-hybrid structure by RACE experiments on endogenous troponin I antisense RNA. RNA10, 1215–1224.10.1261/rna.5261204Search in Google Scholar
Bernstein, E., Caudy, A. A., Hammond, S. M., and Hannon, G. J. (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature409, 363–366.10.1038/35053110Search in Google Scholar
Billy, E., Brondani, V., Zhang, H., Muller, U., and Filipowicz, W. (2001). Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc. Natl. Acad. Sci. USA98, 14428–14433.10.1073/pnas.261562698Search in Google Scholar
Dsouza, M., Larsen, N., and Overbeek, R. (1997). Searching for patterns in genomic data. Trends Genet.13, 497–498.10.1016/S0168-9525(97)01347-4Search in Google Scholar
Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature411, 494–498.10.1038/35078107Search in Google Scholar
Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., and Mello, C. C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature391, 806–811.10.1038/35888Search in Google Scholar
Glockner, G., Eichinger, L., Szafranski, K., Pachebat, J. A., Bankier, A. T., Dear, P. H., Lehmann, R., Baumgart, C., Parra, G., Abril, J. F. et al. (2002). Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature418, 79–85.10.1038/nature00847Search in Google Scholar
Glockner, G., Szafranski, K., Winckler, T., Dingermann, T., Quail, M. A., Cox, E., Eichinger, L., Noegel, A. A., and Rosenthal, A. (2001). The complex repeats of Dictyostelium discoideum. Genome Res.11, 585–594.10.1101/gr.162201Search in Google Scholar
Hildebrandt, M. and Nellen, W. (1992). Differential antisense transcription from the Dictyostelium EB4 gene locus-implications on antisense-mediated regulation of messenger RNA stability. Cell69, 124–204.Search in Google Scholar
Jeanmougin, F., Thompson, J. D., Gouy, M., Higgins, D. G., Gibson, T. J. (1998). Multiple sequence alignment with Clustal X. Trends Biochem. Sci.23, 403–405.10.1016/S0968-0004(98)01285-7Search in Google Scholar
Kulikova, T., Aldebert, P., Althorpe, N., Baker, W., Bates, K., Browne, P., van den Broek, A., Cochrane, G., Duggan, K., Eberhardt, R. et al. (2004). The EMBL Nucleotide Sequence Database. Nucleic Acids Res.32 (database issue), D27–30.10.1093/nar/gkh120Search in Google Scholar PubMed PubMed Central
Lavorgna, G., Dahary, D., Lehner, B., Sorek, R., Sanderson, C. M., and Casari, G. (2004). In search of antisense. Trends Biochem. Sci.29, 88–94.10.1016/j.tibs.2003.12.002Search in Google Scholar
Lehner, B., Williams, G., Campbell, R. D., and Sanderson, C. M. (2002). Antisense transcripts in the human genome. Trends Genet.18, 63–65.10.1016/S0168-9525(02)02598-2Search in Google Scholar
Manche, L., Green, S. R., Schmedt, C., and Mathews, M. B. (1992). Interactions between double-stranded RNA regulators and the protein kinase DAI. Mol. Cell. Biol.12, 5238–48.Search in Google Scholar
Martens, H., Novotny, J., Oberstrass, J., Steck, T. L., Postlethwait, P., and Nellen, W. (2002). RNAi in Dictyostelium: the role of RNA-directed RNA polymerases and double-stranded RNase. Mol. Biol. Cell13, 445–453.10.1091/mbc.01-04-0211Search in Google Scholar
Novotny, J., Diegel, S., Schirmacher, H., Mohrle, A., Hildebrandt, M., Oberstrass, J., and Nellen, W. (2001). Dictyostelium double-stranded ribonuclease. Methods Enzymol.342, 193–212.10.1016/S0076-6879(01)42545-6Search in Google Scholar
Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G., Korf, I., Lapp, H. et al. (2002). The Bioperl toolkit: perl modules for the life sciences. Genome Res.12, 1611–1618.10.1101/gr.361602Search in Google Scholar
Tomari, Y., Du, T., Haley, B., Schwarz, D. S., Bennett, R., Cook, H. A., Koppetsch, B. S., Theurkauf, W. E., and Zamore, P. D. (2004). RISC assembly defects in the Drosophila RNAi mutant armitage. Cell116, 831–841.10.1016/S0092-8674(04)00218-1Search in Google Scholar
Zamore, P. D., Tuschl, T., Sharp, P. A., and Bartel, D. P. (2000). RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell101, 25–33.10.1016/S0092-8674(00)80620-0Search in Google Scholar
Zdobnov, E. M., and Apweiler, R. (2001). InterProScan – an integration platform for the signature-recognition methods in InterPro. Bioinformatics17, 847–848.10.1093/bioinformatics/17.9.847Search in Google Scholar PubMed
Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res.31, 3406–3415.10.1093/nar/gkg595Search in Google Scholar PubMed PubMed Central
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