A database search for double-strand containing RNAs in Dictyostelium discoideum

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.

[1]  M. Mathews,et al.  Interactions between double-stranded RNA regulators and the protein kinase DAI , 1992, Molecular and cellular biology.

[2]  Wolfgang Nellen,et al.  Differential antisense transcription from the Dictyostelium EB4 gene locus: Implications on antisense-mediated regulation of mRNA stability , 1992, Cell.

[3]  R. Overbeek,et al.  Searching for patterns in genomic data. , 1997, Trends in genetics : TIG.

[4]  J. Thompson,et al.  Multiple sequence alignment with Clustal X. , 1998, Trends in biochemical sciences.

[5]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[6]  P. Sharp,et al.  RNAi Double-Stranded RNA Directs the ATP-Dependent Cleavage of mRNA at 21 to 23 Nucleotide Intervals , 2000, Cell.

[7]  Vincent Lombard,et al.  The EMBL Nucleotide Sequence Database , 2005, Nucleic Acids Res..

[8]  W. Filipowicz,et al.  Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[9]  M. Quail,et al.  The complex repeats of Dictyostelium discoideum. , 2001, Genome research.

[10]  A. Caudy,et al.  Role for a bidentate ribonuclease in the initiation step of RNA interference , 2001 .

[11]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[12]  S. Diegel,et al.  Dictyostelium double-stranded ribonuclease. , 2001, Methods in enzymology.

[13]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[14]  T. Steck,et al.  RNAi in Dictyostelium: the role of RNA-directed RNA polymerases and double-stranded RNase. , 2002, Molecular biology of the cell.

[15]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[16]  Matthias Platzer,et al.  Sequence and analysis of chromosome 2 of Dictyostelium discoideum , 2002, Nature.

[17]  Ben Lehner,et al.  Antisense transcripts in the human genome. , 2002, Trends in genetics : TIG.

[18]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[19]  I. Morano,et al.  Detection of a novel sense-antisense RNA-hybrid structure by RACE experiments on endogenous troponin I antisense RNA. , 2004, RNA.

[20]  T. Du,et al.  RISC Assembly Defects in the Drosophila RNAi Mutant armitage , 2004, Cell.

[21]  Ben Lehner,et al.  In search of antisense. , 2004, Trends in biochemical sciences.