title: Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs).
abstract: 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.
authors: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.
authors: Cheng
authors: C
authors: Lu
authors: Dong-Hoon
authors: DH
authors: Jeong
authors: Karthik
authors: K
authors: Kulkarni
authors: Manoj
authors: M
authors: Pillay
authors: Kan
authors: K
authors: Nobuta
authors: Rana
authors: R
authors: German
authors: Shawn R
authors: SR
authors: Thatcher
authors: Christopher
authors: C
authors: Maher
authors: Lifang
authors: L
authors: Zhang
authors: Doreen
authors: D
authors: Ware
authors: Bin
authors: B
authors: Liu
authors: Xiaofeng
authors: X
authors: Cao
authors: Blake C
authors: BC
authors: Meyers
authors: Pamela J
authors: PJ
authors: Green
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics*; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D016372:RNA, Antisense / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D016372:RNA, Antisense; D012333:RNA, Messenger