title: Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants.
abstract: Plant microRNAs (miRNAs) are predominantly 21 nucleotides (nt) long but non-canonical lengths of 22 and 20 nt are commonly observed in diverse plant species. While miRNAs longer than 21 nt can be attributed to the neglect of unpaired bases within asymmetric bulges by the ruler function of dicer-like 1 (DCL1), how 20-nt miRNA is generated remains obscure. Analysis of small RNA data revealed that 20-nt miRNA can be divided into 3 main groups featured by atypical 3' overhangs or shorter duplex regions. Asymmetric bulges or mismatches at specific positions are commonly observed within each group and were shown to be crucial for 20-nt miRNA formation. Analysis of DCL1 cleavage sites on 20-nt miRNA precursors suggests that these determinants might alter precursor structure or trigger 3'-end decay of mature miRNA. The results herein advance our understanding of miRNA biogenesis and demonstrate that the effect of asymmetric bulges on miRNA length could be position-dependent.
authors.affiliation: a Agricultural Biotechnology Research Center; Academia Sinica ; Taipei , Taiwan.
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Lee
authors.affiliation: a Agricultural Biotechnology Research Center; Academia Sinica ; Taipei , Taiwan.
authors.forename: Shin-Hua
authors.initials: SH
authors.lastname: Lu
authors.affiliation: b Jianguo Municipal High School ; Taipei , Taiwan.|c Institute of Plant and Microbial Biology; Academia Sinica ; Taipei , Taiwan.|d Present affiliations:School of Medicine; National Taiwan University; Taipei, Taiwan.
authors.forename: Ming-Hsuan
authors.initials: MH
authors.lastname: Lu
authors.affiliation: a Agricultural Biotechnology Research Center; Academia Sinica ; Taipei , Taiwan.|e Institute of Ecology and Evolutionary Biology; National Taiwan University; Taipei, Taiwan.
authors.forename: Chen-Jui
authors.initials: CJ
authors.lastname: Yang
authors.affiliation: c Institute of Plant and Microbial Biology; Academia Sinica ; Taipei , Taiwan.
authors.forename: Shu-Hsing
authors.initials: SH
authors.lastname: Wu
authors.affiliation: a Agricultural Biotechnology Research Center; Academia Sinica ; Taipei , Taiwan.
authors.forename: Ho-Ming
authors.initials: HM
authors.lastname: Chen
mesh_terms: D020137:Base Pair Mismatch; D020029:Base Pairing; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics*; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes; D010944:Plants / Q000235:genetics*; D012323:RNA Processing, Post-Transcriptional; D018749:RNA, Plant; D043244:Ribonuclease III / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D009692:Nucleic Acid Heteroduplexes; D018749:RNA, Plant; D043244:Ribonuclease III
keywords: DICER-LIKE 1; asymmetric bulge; microRNA duplex; microRNA length; mismatch