Genome-wide analysis for rice small RNAs by MPSS

Small RNAs (21-24 nt) 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 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 Keywords: small RNA sequencing by MPSS Six rice samples are included in this study. They are 1) immature panicles, 2) germinating seedlings (control for Magnaporthe treatment), 3) germinating seedlings infected with Magnaporthe grisea,4)stems, 5) three-week-old seedlings (control for ABA treatment), 6) three-week-old seedlings treated with ABA.