title: Genome-wide identification of reverse complementary microRNA genes in plants.
abstract: MicroRNAs (miRNAs) are ∼21-nucleotide small RNAs (sRNAs) with essential regulatory roles in plants. They are generated from stem-loop-structured precursors through two sequential Dicer-like 1 (DCL1)-mediated cleavages. To date, hundreds of plant miRNAs have been uncovered. However, the question, whether the sequences reverse complementary (RC) to the miRNA precursors could form hairpin-like structures and produce sRNA duplexes similar to the miRNA/miRNA* pairs has not been solved yet. Here, we interrogated this possibility in 16 plant species based on sRNA high-throughput sequencing data and secondary structure prediction. A total of 59 RC sequences with great potential to form stem-loop structures and generate miRNA/miRNA*-like duplexes were identified in ten plants, which were named as RC-miRNA precursors. Unlike the canonical miRNAs, only a few cleavage targets of the RC-miRNAs were identified in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), and none in Soybean (Glycine max) based on degradome data. Surprisingly, the genomic regions surrounding some of the RC-miRNA target recognition sites were observed to be specifically methylated in both Arabidopsis and rice. Taken together, we reported a new class of miRNAs, called RC-miRNAs, which were generated from the antisense strands of the miRNA precursors. Based on the results, we speculated that the mature RC-miRNAs might have subtle regulatory activity through target cleavages, but might possess short interfering RNA-like activity by guiding sequence-specific DNA methylation.
authors.affiliation: College of Life Sciences, Huzhou Teachers College, Huzhou, The People's Republic of China.
authors.forename: Chaogang
authors.initials: C
authors.lastname: Shao
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Ma
authors.forename: Xiufang
authors.initials: X
authors.lastname: Xu
authors.forename: Huizhong
authors.initials: H
authors.lastname: Wang
authors.forename: Yijun
authors.initials: Y
authors.lastname: Meng
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant