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Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins

Francisco Merchan12, Adnane Boualem3*, Martin Crespi1* and Florian Frugier1

Author Affiliations

1 Institut des Sciences du Végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Avenue de la terrasse, 91198 Gif sur Yvette cedex, France

2 Current address: Dto Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, C/Profesor García González 2, 41012 Sevilla, Spain

3 Unité de recherche en Génomique Végétale (URGV), Institut National de la Recherche Agronomique (INRA), Rue Gaston Crémieux, 91057 Evry cedex, France

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Genome Biology 2009, 10:R136  doi:10.1186/gb-2009-10-12-r136

Published: 1 December 2009



MicroRNAs (miRNAs) are endogenous single-stranded small RNAs that regulate the expression of specific mRNAs involved in diverse biological processes. In plants, miRNAs are generally encoded as a single species in independent transcriptional units, referred to as MIRNA genes, in contrast to animal miRNAs, which are frequently clustered.


We performed a comparative genomic analysis in three model plants (rice, poplar and Arabidopsis) and characterized miRNA clusters containing two to eight miRNA species. These clusters usually encode miRNAs of the same family and certain share a common evolutionary origin across monocot and dicot lineages. In addition, we identified miRNA clusters harboring miRNAs with unrelated sequences that are usually not evolutionarily conserved. Strikingly, non-homologous miRNAs from the same cluster were predicted to target transcripts encoding related proteins. At least four Arabidopsis non-homologous clusters were expressed as single transcriptional units. Overexpression of one of these polycistronic precursors, producing Ath-miR859 and Ath-miR774, led to the DCL1-dependent accumulation of both miRNAs and down-regulation of their different mRNA targets encoding F-box proteins.


In addition to polycistronic precursors carrying related miRNAs, plants also contain precursors allowing coordinated expression of non-homologous miRNAs to co-regulate functionally related target transcripts. This mechanism paves the way for using polycistronic MIRNA precursors as a new molecular tool for plant biologists to simultaneously control the expression of different genes.