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

Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently [almost equal to]240 microRNAs (miRNAs) have been annotated. We sequenced more than four million small RNAs from rice and identified another 2...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2008-03, Vol.105 (12), p.4951-4956
Main Authors: Lu, Cheng, Jeong, Dong-Hoon, Kulkarni, Karthik, Pillay, Manoj, Nobuta, Kan, German, Rana, Thatcher, Shawn R, Maher, Christopher, Zhang, Lifang, Ware, Doreen, Liu, Bin, Cao, Xiaofeng, Meyers, Blake C, Green, Pamela J
Format: Article
Language:English
Subjects:
antisense microRNA
antisense RNA
Base Sequence
Biological Sciences
Botany
Conserved Sequence
Gene Expression Regulation, Plant
Gene Library
Genes
Genetic loci
Genome, Plant - genetics
Genomics
introns
Libraries
loci
Messenger RNA
MicroRNA
MicroRNAs - biosynthesis
MicroRNAs - chemistry
MicroRNAs - genetics
Models, Biological
Molecular Sequence Data
Nucleic Acid Conformation
nucleotide sequences
Oryza - genetics
Oryza sativa
Plant Proteins - genetics
Plant Proteins - metabolism
Ribonucleic acid
Rice
RNA
RNA, Antisense - genetics
RNA, Messenger - genetics
RNA, Messenger - metabolism
Sequencing
Signatures
Small interfering RNA
Studies
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Summary:Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently [almost equal to]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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0708743105