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

Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4951-6. doi: 10.1073/pnas.0708743105. Epub 2008 Mar 19.


Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently approximately 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Conserved Sequence
  • Gene Expression Regulation, Plant
  • Gene Library
  • Genome, Plant / genetics*
  • MicroRNAs / biosynthesis
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • Models, Biological
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Oryza / genetics*
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • RNA, Antisense / genetics*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism


  • MicroRNAs
  • Plant Proteins
  • RNA, Antisense
  • RNA, Messenger

Associated data

  • GEO/GSE10523