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Briefings in Bioinformatics 2005 6(1):72-85; doi:10.1093/bib/6.1.72
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© Henry Stewart Publications

Additional Paper

Current efforts in the analysis of RNAi and RNAi target genes

Peter Bengert
Undertakes research aimed at understanding and predicting regulatory interactions mediated by RNA structures

Thomas Dandekar
Head of Bioinformatics Department at the Biocenter in Würzburg; further collaborations and research with Peter Bengert are undertaken at BZH and EMBL in Heidelberg. Thomas Dandekar's further research interests are modelling of protein structures and cellular interaction networks


Thomas Dandekar, Department of Bioinformatics, Biocenter, Am Hubland, University of Wurzburg, Germany Tel: +49 93 1888 4551 Fax: +49 93 1888 4552 E-mail: dandekar{at}biozentrum.uniwuerzburg.de

RNAi is RNA interference by short RNAs. It influences gene-expression by down-regulation of mRNAs, typically by complementarity to the 3' UTR (untranslated region) of the mRNA. microRNAs (miRNAs) are short RNAs acting as natural RNAi. miRNAs mediate down regulation of many mRNAs from developmental genes and transcription factor genes. Natural examples for this additional level of post-transcriptional control are increasing. Suitable computer-based search strategies for new miRNA candidates include precursor folding as well as different compositional search strategies. Example programs for this are presented. New own and other data are provided for an overview on such strategies. A strategy feasible in plants for miRNA target identification is direct base pairing of miRNAs to potential mRNA target 3' UTRs. Correct identification in animals usually requires comparative genomics and conserved UTR regions pairing to conserved miRNA substructures. A number of example programs and target examples for these tasks are examined. Finally, strategies and programs for artificial gene silencing by designed RNAi are explained.

Keywords: miRNA, RNA folding, RNAi, RNA structure, database, RNA motif


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