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Target prediction for small, noncoding RNAs in bacteria

Tjaden, Brian and Goodwin, Sarah S. and Opdyke, Jason A. and Guillier, Maude and Fu, Daniel X. and Gottesman, Susan and Storz, Gisela (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Research, 34 (9). pp. 2791-2802. ISSN 0305-1048. doi:10.1093/nar/gkl356.

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Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a limited number of the corresponding mRNA targets have been identified. Here we present a program, TargetRNA, that predicts the targets of these bacterial RNA regulators. The program was evaluated by assessing whether previously known targets could be identified. The program was then used to predict targets for the Escherichia coli RNAs RyhB, OmrA, OmrB and OxyS, and the predictions were compared with changes in whole genome expression patterns observed upon expression of the sRNAs. Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs.

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Additional Information:© The Author 2006. Published by Oxford University Press. Reprinted with permission. Received February 2, 2006. Revised April 5, 2006. Accepted April 20, 2006. We thank E. Massé for sharing his microarray results and P. Clote, D. FitzGerald, P. FitzGerald and E. Massé for comments on the manuscript. This work was supported by the Intramural Research Program of the NIH (NICHD and NCI). B.T. is supported by a Brachman Hoffman Fellowship at Wellesley College. Funding to pay the Open Access publication charges for this article was provided by Wellesley College. Conflict of interest statement. None declared. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
Issue or Number:9
Record Number:CaltechAUTHORS:TJAnar06
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:3215
Deposited By: Archive Administrator
Deposited On:22 May 2006
Last Modified:08 Nov 2021 19:54

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