Research article

Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

Séverine Lacombe^{* 1} , Hiroshi Nagasaki^{* 2} , Carole Santi^{* 1} , David Duval¹ , Benoît Piégu¹ , Martine Bangratz¹ , Jean-Christophe Breitler³ , Emmanuel Guiderdoni³ , Christophe Brugidou¹ , Judith Hirsch⁴ , Xiaofeng Cao⁵ , Claire Brice¹ , Olivier Panaud¹ , Wojciech M Karlowski⁶ , Yutaka Sato² and Manuel Echeverria¹

¹Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan via Domitia – CNRS-IRD, 52, Av. Paul Alduy, 66860 Perpignan Cedex, France

²Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan

³DAP, UMR 1098, Université de Montpellier II-CIRAD-INRA-SUPAGRO 2477 Avenue Agropolis, F-34398 Montpellier Cedex 5, France

⁴INRA-SUPAGRO, UMR BGPI, Campus Baillarguet, F-34398 Montpellier Cedex 05, France

⁵State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China

⁶Bioinformatic Laboratory, A. Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland

author email corresponding author email* Contributed equally

BMC Plant Biology 2008, 8:123doi:10.1186/1471-2229-8-123

Published:	2 December 2008

Abstract

Background

The plant miRNAs represent an important class of endogenous small RNAs that guide cleavage of an mRNA target or repress its translation to control development and adaptation to stresses. MiRNAs are nuclear-encoded genes transcribed by RNA polymerase II, producing a primary precursor that is subsequently processed by DCL1 an RNase III Dicer-like protein.

In rice hundreds of miRNAs have been described or predicted, but little is known on their genes and precursors which are important criteria to distinguish them from siRNAs. Here we develop a combination of experimental approaches to detect novel miRNAs in rice, identify their precursor transcripts and genes and predict or validate their mRNA targets.

Results

We produced four cDNA libraries from small RNA fractions extracted from distinct rice tissues. By in silico analysis we selected 6 potential novel miRNAs, and confirmed that their expression requires OsDCL1. We predicted their targets and used 5'RACE to validate cleavage for three of them, targeting a PPR, an SPX domain protein and a GT-like transcription factor respectively.

In addition, we identified precursor transcripts for the 6 miRNAs expressed in rice, showing that these precursors can be efficiently processed using a transient expression assay in transfected Nicotiana benthamiana leaves. Most interestingly, we describe two precursors producing tandem miRNAs, but in distinct arrays. We focus on one of them encoding osa-miR159a.2, a novel miRNA produced from the same stem-loop structure encoding the conserved osa-miR159a.1. We show that this dual osa-miR159a.2-osa-miR159a.1 structure is conserved in distant rice species and maize. Finally we show that the predicted mRNA target of osa-miR159a.2 encoding a GT-like transcription factor is cleaved in vivo at the expected site.

Conclusion

The combination of approaches developed here identified six novel miRNAs expressed in rice which can be clearly distinguished from siRNAs. Importantly, we show that two miRNAs can be produced from a single precursor, either from tandem stem-loops or tandemly arrayed in a single stem-loop. This suggests that processing of these precursors could be an important regulatory step to produce one or more functional miRNAs in plants and perhaps coordinate cleavage of distinct targets in the same plant tissue.