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Nucleic Acids Research Advance Access originally published online on October 8, 2008
Nucleic Acids Research 2008 36(20):6429-6438; doi:10.1093/nar/gkn670
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Nucleic Acids Research, 2008, Vol. 36, No. 20 6429-6438
© 2008 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

Evolution of Arabidopsis MIR genes generates novel microRNA classes

Franck Vazquez1,2,*, Todd Blevins1, Jérôme Ailhas1, Thomas Boller2 and Frederick Meins, Jr1

1Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Maulbeerstrasse 66, 4058 Basel and 2Botanical Institute, Zurich-Basel Plant Science Center, Basel University, Hebelstrasse 1, 4056 Basel, Switzerland

*To whom correspondence should be addressed. Tel: +41 61 267 35 17; Fax: +41 61 267 23 30; Email: franck.vazquez{at}unibas.ch

Received July 23, 2008. Revised September 18, 2008. Accepted September 22, 2008.

In Arabidopsis, canonical 21-nt miRNAs are generated by Dicer-like (DCL) 1 from hairpin precursors. We have identified a novel class of functional 23- to 25-nt long-miRNAs that is generated independently from the same miRNA precursors by DCL3. Long-miRNAs are developmentally regulated and in some cases have been conserved during evolution implying that they have biological functions. Plant microRNA genes (MIR) have been proposed to evolve by inverted duplication of the target gene. We found that recently evolved MIR genes consistently give rise to long-miRNAs, while ancient MIR genes give rise predominantly to canonical miRNAs. Transcripts from inverted repeats representing evolving proto-MIR genes were processed by DCL3 into long-miRNAs and also by DCL1, DCL2 or DCL4 depending on hairpin stem length to produce different sizes of miRNAs. Our results suggest that evolution of MIR genes is associated with gradual, overlapping changes in DCL usage resulting in specific size classes of miRNAs.

Present addresses: Todd Blevins, Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA Jérôme Ailhas, ROOTec Bioactives AG, Benkenstrasse 254, Pavillon B, TZW, 4108 Witterswil, Switzerland


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