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 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.
Lu
Cheng
C
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.
Jeong
Dong-Hoon
DH
Kulkarni
Karthik
K
Pillay
Manoj
M
Nobuta
Kan
K
German
Rana
R
Thatcher
Shawn R
SR
Maher
Christopher
C
Zhang
Lifang
L
Ware
Doreen
D
Liu
Bin
B
Cao
Xiaofeng
X
Meyers
Blake C
BC
Green
Pamela J
PJ
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
D035683:MicroRNAs; D010940:Plant Proteins; D016372:RNA, Antisense; D012333:RNA, Messenger