@InProceedings{Richter:Backofen:Acces_conse_bacte:2011,
  author =      {Richter, Andreas S. and Backofen, Rolf},
  title =       {Accessibility and conservation in bacterial small {RNA}-{mRNA}
                 interactions and implications for genome-wide target
                 predictions},
  booktitle =   {Proceedings of the German Conference on Bioinformatics (GCB
                 2011)},
  year =        {2011},
  abstract =    {Bacterial small RNAs (sRNAs) are a class of structural RNAs
that often regulate mRNA targets via post-transcriptional base pair
interactions. In this study, we assessed the accessibility and conservation of
the interaction sites and the influence of these features on genome-wide target
predictions. For this purpose, we compiled a set of 71 experimentally verified
sRNA-target pairs from \textit{Escherichia coli} and \textit{Salmonella}, and
collected genome-wide information on 5'~untranslated regions of annotated genes.
Then, features of the confirmed interactions were compared to a set of
non-interactions.
We found that the interaction sites both in sRNA and target are more accessible
than in the negative data. Furthermore, interaction sites in the sRNAs, but not
in the targets, show high sequence conservation. The base pairing between sRNA
and target was not found to be generally conserved across more distantly related
species. We then present two approaches to constrain the region of interaction
initiation to (1) well-accessible regions in both interaction partners or (2)
unstructured conserved sRNA regions derived from reliability profiles of
multiple sRNA alignments. Using these constraints, genome-wide target
predictions were improved in terms of specificity.},
  user =	 {arichter}
}