Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 03-015

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Titel:
Conserved RNA Secondary Structures in Flaviviridae Genomes

Author(s):
Caroline Thurner, Christina Witwer, Ivo L. Hofacker, Peter F. Stadler,

Abstract:
We report here on a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This virus family consists of the three genera Flavivirus, Pestivirus, Hepacivirus and the group of \emph{Hepatitis G Viruses} with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered separately: The genus Flavivirus with its type I cap structure at the 5' untranslated region (UTR) and a highly structured 3'UTR, and the remaining three groups that exhibit translation control by means of a Internal Ribosomal Entry Site (IRES) in the 5'UTR and a much shorter less structured 3'UTR. The main findings of our survey are: strong evidence for the possibility of genome cyclization in Hepatitis C and G viruses in addition to the Flaviviruses; a surprisingly large number of conserved RNA motifs in the coding regions; and a lower level of detailed structural conservation in the IRES and 3'UTR motifs than reported in the literature. An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements.

Keywords:
Flaviviridae, RNA secondary structure, Internal Ribosomal Entry Site (IRES), Genome Cyclization.

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