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First published online July 16, 2004; 10.1105/tpc.104.022830

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The Plant Cell 16:2001-2019 (2004)
© 2004 American Society of Plant Biologists

Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis

Ramanjulu Sunkar and Jian-Kang Zhu1

Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521

1 To whom correspondence should be addressed. E-mail jian-kang.zhu{at}ucr.edu; fax 909-827-7115.

MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are small noncoding RNAs that have recently emerged as important regulators of mRNA degradation, translational repression, and chromatin modification. In Arabidopsis thaliana, 43 miRNAs comprising 15 families have been reported thus far. In an attempt to identify novel and abiotic stress regulated miRNAs and siRNAs, we constructed a library of small RNAs from Arabidopsis seedlings exposed to dehydration, salinity, or cold stress or to the plant stress hormone abscisic acid. Sequencing of the library and subsequent analysis revealed 26 new miRNAs from 34 loci, forming 15 new families. Two of the new miRNAs from three loci are members of previously reported miR171 and miR319 families. Some of the miRNAs are preferentially expressed in specific tissues, and several are either upregulated or downregulated by abiotic stresses. Ten of the miRNAs are highly conserved in other plant species. Fifty-one potential targets with diverse function were predicted for the newly identified miRNAs based on sequence complementarity. In addition to miRNAs, we identified 102 other novel endogenous small RNAs in Arabidopsis. These findings suggest that a large number of miRNAs and other small regulatory RNAs are encoded by the Arabidopsis genome and that some of them may play important roles in plant responses to environmental stresses as well as in development and genome maintenance.


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