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Bioinformatics Advance Access published online on October 22, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp609
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

Andreas S. Richter 1, Christian Schleberger 2, Rolf Backofen 1,* and Claudia Steglich 3,*

1 Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 106, Freiburg D-79110, Germany
2 Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Str. 19, Freiburg D-79104, Germany
3 Genetics & Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg D-79104, Germany

*To whom correspondence should be addressed. Rolf Backofen, E-mail: backofen{at}informatik.uni-freiburg.de


  Abstract

Motivation: Prochlorococcus possesses the smallest genome of all sequenced photoautotrophs. Although the number of regulatory proteins in the genome is very small, the relative number of small regulatory RNAs is comparable to that of other bacteria. The compact genome size of Prochlorococcus offers an ideal system to search for targets of small RNAs and to refine existing target prediction algorithms.

Results: Target predictions for the cyanobacterial small RNA Yfr1 were carried out with INTARNA in Prochlorococcus MED4. The ultraconserved Yfr1 sequence motif was defined as the putative interaction seed. To study the impact of Yfr1 on its predicted mRNA targets, a reporter system based on green fluorescent protein (GFP) was applied. We show that Yfr1 inhibits the translation of two predicted targets. We used mutation analysis to confirm that Yfr1 directly regulates its targets by an antisense interaction sequestering the ribosome binding site, and to assess the importance of interaction site accessibility.

Contact: backofen{at}informatik.uni-freiburg.de, claudia.steglich{at}biologie.uni-freiburg.de

Associate Editor: Prof. Ivo Hofacker

Received on July 20, 2009; revised on September 18, 2009; accepted on October 11, 2009

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