title: Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis.
abstract: Plant microRNA (miRNA) is a crucial regulator of gene expression. It has been reported that more than one miRNA/miRNA duplex could be produced from a microRNA precursor (pre-miRNA). In this study, we performed a comprehensive search for the novel miRNA candidates on the pre-miRNAs of Arabidopsis. AGO1 enrichment, co-existence of the miRNA-like coordinates, and unique genome-wide match sites were taken into consideration for candidate screening. As a result, 43 miRNA-like candidates derived from 25 pre-miRNAs were identified. Among these candidates, 31 strong candidates from 22 pre-miRNAs passed all the filtering steps. Interestingly, some of these miRNA-like candidates showed organ-specific expression patterns. After target prediction and degradome sequencing data-based validation, five miRNA candidate-target pairs (ath-miR863-5p.2-AT1G76550.1, ath-miR822.2-AT5G03552.1, ath-miR822.3-AT5G02350.1, sRNA4-AT1G66290.1 and sRNA6-AT1G66310.1) were identified, providing a basis for in-depth functional analysis of these miRNA candidates. These results could update the current understanding of the biogenesis and the action of the plant miRNAs.
authors.affiliation: College of Life Sciences, Huzhou Teachers College, Huzhou 313000, PR China.
authors.forename: Chaogang
authors.initials: C
authors.lastname: Shao
authors.forename: Qianer
authors.initials: Q
authors.lastname: Wu
authors.forename: Jinjin
authors.initials: J
authors.lastname: Qiu
authors.forename: Shaohua
authors.initials: S
authors.lastname: Jin
authors.forename: Beilun
authors.initials: B
authors.lastname: Zhang
authors.forename: Jian
authors.initials: J
authors.lastname: Qian
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.forename: Yijun
authors.initials: Y
authors.lastname: Meng
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors
keywords: AGO1; Arabidopsis; Argonaute 1; Argonaute 1 (AGO1); Degradome; GEO; Gene Expression Omnibus; HTS; Long-stem pre-miRNA (precursor microRNA); MicroRNA*-like; MicroRNA-like-coding site; RPM; TAIR; The Arabidopsis Information Resource; U; high-throughput sequencing; isomiR; miRNA; microRNA; microRNA isomer; nt; nucleotide; pre-miRNA; precursor microRNA; reads per million; sRNA; small RNA; t-plot; target plot; uridine