Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)

^†Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711;
^‡Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
^§Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794;
^¶North Atlantic Area Plant, Soil, and Nutrition Laboratory Research Unit, U.S. Department of Agriculture/Agricultural Research Service, Ithaca, NY 15853; and
^‖National Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100080, China

Edited by Xiaoyu Zhang, University of Georgia, Athens, GA, and accepted by the Editorial Board January 15, 2008 (received for review September 14, 2007)

Abstract

Small RNAs (21–24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ≈240 microRNAs (miRNAs) have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a unique class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. We provide evidence that the miRNAs function by inducing mRNA cleavage in the middle of their complementary site. Their production requires Dicer-like 1 (DCL1) activity, which is essential for canonical miRNA biogenesis. All of the natural antisense miRNAs (nat-miRNAs) identified in this study have large introns in their precursors that appear critical for nat-miRNA evolution and for the formation of functional miRNA loci. These findings suggest that other natural cis-antisense loci with similar exon–intron arrangements could be another source of miRNA genes.

Footnotes

^††To whom correspondence should be addressed. E-mail: green{at}dbi.udel.edu
Author contributions: C.L., D.-H.J., B.C.M., and P.J.G. designed research; C.L., D.-H.J., R.G., and S.R.T. performed research; C.M., L.Z., D.W., B.L., and X.C. contributed new reagents/analytic tools; C.L., D.-H.J., K.K., M.P., K.N., B.C.M., and P.J.G. analyzed data; and C.L., B.C.M., and P.J.G. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission. X.Z. is a guest editor invited by the Editorial Board.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE10523).
This article contains supporting information online at www.pnas.org/cgi/content/full/0708743105/DC1.
Freely available online through the PNAS open access option.