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

Cheng Lu, Dong Hoon Jeong, Karthik Kulkarni, Manoj Pillay, Kan Nobuta, Rana German, Shawn R. Thatcher, Christopher Maher, Lifang Zhang, Doreen Ware, Bin Liu, Xiaofeng Cao, Blake C. Meyers, Pamela J. Green

Research output: Contribution to journalArticlepeer-review

177 Scopus citations


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.

Original languageEnglish
Pages (from-to)4951-4956
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number12
StatePublished - Mar 25 2008


  • High-throughput sequencing
  • Massively parallel signature sequencing (MPSS)
  • Small RNA
  • siRNA


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