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Int. J. Mol. Sci. 2012, 13(12), 16223-16240; doi:10.3390/ijms131216223

Modelling Translation Initiation under the Influence of sRNA

* ,
Institute for Theoretical Chemistry, University Vienna, Währingerstraße 17, 1090 Vienna, Austria
* Author to whom correspondence should be addressed.
Received: 21 October 2012 / Revised: 21 November 2012 / Accepted: 27 November 2012 / Published: 30 November 2012
(This article belongs to the Special Issue Non-Coding RNAs 2012)
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Bacterial small non-coding RNA (sRNA) plays an important role in post-transcriptional gene regulation. Although the number of annotated sRNA is steadily increasing, their functional characterization is still lagging behind. Various computational strategies for finding sRNA–mRNA interactions, and thus putative sRNA targets, were developed. Most of them suffer from a high false positive rate. Here, we present a qualitative model to simulate the effect of an sRNA on the translation initiation of a potential target. Information about the ribosome–mRNA interaction, sRNA–mRNA interaction and expression information from deep sequencing experiments is integrated to calculate the change in translation initiation complex formation, as a proxy for translational activity. This model can be used to post-evaluate predicted targets, hence condensing the list of potential targets. We show that our translation initiation model, under the influence of an sRNA, can successfully simulate thirteen out of fifteen tested sRNA–mRNA interactions in a qualitative manner. To show the gain in specificity, we applied our method to a target search for the Escherichia coli sRNA RyhB. Compared with simple target prediction without post-evaluation, we reduce the number of targets to less than one fourth potential targets, considerably reducing the burden of experimental validation.
Keywords: sRNA; sRNA target prediction; translation initiation sRNA; sRNA target prediction; translation initiation
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Amman, F.; Flamm, C.; Hofacker, I. Modelling Translation Initiation under the Influence of sRNA. Int. J. Mol. Sci. 2012, 13, 16223-16240.

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