Reference "Cloning and Characterization of MicroRNAs from Rice"

Reference ID

9500

Title

Cloning and Characterization of MicroRNAs from Rice

Source

The Plant cell, 2005, vol. 17, pp. 1397-1411

Authors (4)

Sunkar-R	Girke-T
Jain-P-K	Zhu-J-K

Abstract

MicroRNAs (miRNAs) are a growing family of small noncoding RNAs that
downregulate gene expression in a sequence-specific manner. The identification
of the entire set of miRNAs from a model organism is a critical step toward
understanding miRNA-guided gene regulation. Rice (Oryza sativa) and Arabidopsis
thaliana, two plant model species with fully sequenced genomes, are
representatives of monocotyledonous and dicotyledonous flowering plants,
respectively. Thus far, experimental identification of miRNAs in plants has been
confined to Arabidopsis. Computational analysis based on conservation with known
miRNAs from Arabidopsis has predicted 20 families of miRNAs in rice. To identify
miRNAs that are difficult to predict in silico or not conserved in Arabidopsis,
we generated three cDNA libraries of small RNAs from rice shoot, root, and
inflorescence tissues. We identified 35 miRNAs, of which 14 are new, and these
define 13 new families. Thirteen of the new miRNAs are not conserved in
Arabidopsis. Four of the new miRNAs are conserved in related monocot species but
not in Arabidopsis, which suggests that these may have evolved after the
divergence of monocots and dicots. The remaining nine new miRNAs appear to be
absent in the known sequences of other plant species. Most of the rice miRNAs
are expressed ubiquitously in all tissues examined, whereas a few display tissue-
specific expression. We predicted 46 genes as targets of the new rice miRNAs: 16
of these predicted targets encode transcription factors, and other target genes
appear to play roles in diverse physiological processes. Four target genes have
been experimentally verified by detection of miRNA-mediated mRNA cleavage. Our
identification of new miRNAs in rice suggests that these miRNAs may have evolved
independently in rice or been lost in other species.