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Nucleic Acids Research Advance Access published online on May 5, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp272
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana

Leonardo Alves-Junior1, Sandra Niemeier1, Arne Hauenschild2, Marc Rehmsmeier2,* and Thomas Merkle1,*

1Genome Research & RNA-based Regulation, Faculty of Biology and 2Bioinformatics of Regulation, Center for Biotechnology (CeBiTec), Bielefeld University, D-33594 Bielefeld, Germany

*To whom correspondence should be addressed. Tel: +43 1 79044 9920; Fax: +43 1 79044 9001; Email: tmerkle{at}cebitec.uni-bielefeld.de Correspondence may also be addressed to Marc Rehmsmeier. Tel: +49 521 106 8723; Fax: +49 521 106 6423; Email: marc.rehmsmeier{at}gmi.oeaw.ac.at

Received May 19, 2008. Revised April 1, 2009. Accepted April 11, 2009.

MicroRNAs (miRNAs) are 20–24 nt long endogenous non-coding RNAs that act as post-transcriptional regulators in metazoa and plants. Plant miRNA targets typically contain a single sequence motif with near-perfect complementarity to the miRNA. Here, we extended and applied the program RNAhybrid to identify novel miRNA targets in the complete annotated Arabidopsis thaliana transcriptome. RNAhybrid predicts the energetically most favorable miRNA:mRNA hybrids that are consistent with user-defined structural constraints. These were: (i) perfect base pairing of the duplex from nucleotide 8 to 12 counting from the 5'-end of the miRNA; (ii) loops with a maximum length of one nucleotide in either strand; (iii) bulges with no more than one nucleotide in size; and (iv) unpaired end overhangs not longer than two nucleotides. G:U base pairs are not treated as mismatches, but contribute less favorable to the overall free energy. The resulting hybrids were filtered according to their minimum free energy, resulting in an overall prediction of more than 600 novel miRNA targets. The specificity and signal-to-noise ratio of the prediction was assessed with either randomized miRNAs or randomized target sequences as negative controls. Our results are in line with recent observations that the majority of miRNA targets are not transcription factors.

Present addresses: Leonardo Alves-Junior, John Innes Centre, Dept. of Cell and Developmental Biology, Norwich Research Park, Colney, Norwich NR4 7UH, UK Marc Rehmsmeier, GMI - Gregor Mendel Institute of Molecular Plant Biology GmbH, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria


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