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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #217766
Title: Genome-wide analysis for discovery of new rice miRNA reveals natural antisense miRNA (nat-miRNAs)

Author
item LU, CHENG - UNIV OF DELAWARE
item JEONG, DONG-HOON - UNIV OF DELAWARE
item KULKARNI, KARTHIK - UNIV OF DELAWARE
item PILLAY, MANOJ - UNIV OF DELAWARE
item NOBUTA, KAN - UNIV OF DELAWARE
item GERMAN, RANA - UNIV OF DELAWARE
item THATCHER, DAWN - UNIV OF DELAWARE
item MAHER, CHRISTOPHER - COLD SPRINGS HARBOR LAB
item ZHANG, LIFANG - COLD SPRINGS HARBOR LAB
item Ware, Doreen
item LIU, BIN - INST OF GENETICS, CAS
item CAO, XIAOFENG - INST OF GENETICS, CAS
item MEYERS, BLAKE - UNIV OF DELAWARE
item GREEN, PAMELA - UNIV OF DELAWARE

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/13/2008
Publication Date: 3/30/2008
Citation: Lu, C., Jeong, D., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, D., Maher, C., Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B., Green, P. 2008. Genome-wide analysis for discovery of new rice miRNA reveals natural antisense miRNA (nat-miRNAs). Proceedings of the National Academy of Sciences. 105(12):4951-4956.

Interpretive Summary: Recently small RNAs have been identified in the gene regulation through inhibition of transcript translation, targeting of transcript cleavage and for directing modification of chromosomes. This paper describes the identification of a novel class of small RNAS based on sequencing small RNAs in rice (nat-miRNAs), derived from natural cis-antisense transcript pairs, where the product of these can match perfectly to their target transcript inducing cleavage. All of these nat-miRNAs have large introns that appear to be important for their evolution and function.

Technical Abstract: Small RNAs (21-24nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 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 novel 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 DCL1 activity, which is essential for canonical miRNA biogenesis. All of the nat-miRNAs identified in this study have large introns in their precursors that appear critical for nat-miRNA evolution and function. These findings reveal that natural cis-antisense gene pairs in eukaryotic genomes could be another source of miRNA genes.