title: Multiple RNA recognition patterns during microRNA biogenesis in plants.
abstract: MicroRNAs (miRNAs) derive from longer precursors with fold-back structures. While animal miRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the evolutionarily conserved miRNAs present in Arabidopsis thaliana. We found that plant miRNAs are processed by four mechanisms, depending on the sequential direction of the processing machinery and the number of cuts required to release the miRNA. Classification of the precursors according to their processing mechanism revealed specific structural determinants for each group. We found that the complexity of the miRNA processing pathways occurs in both ancient and evolutionarily young sequences and that members of the same family can be processed in different ways. We observed that different structural determinants compete for the processing machinery and that alternative miRNAs can be generated from a single precursor. The results provide an explanation for the structural diversity of miRNA precursors in plants and new insights toward the understanding of the biogenesis of small RNAs.
authors.affiliation: IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina;
authors.forename: Nicolás G
authors.initials: NG
authors.lastname: Bologna
authors.forename: Arnaldo L
authors.initials: AL
authors.lastname: Schapire
authors.forename: Jixian
authors.initials: J
authors.lastname: Zhai
authors.forename: Uciel
authors.initials: U
authors.lastname: Chorostecki
authors.forename: Jerome
authors.initials: J
authors.lastname: Boisbouvier
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.forename: Javier F
authors.initials: JF
authors.lastname: Palatnik
mesh_terms: D017360:Arabidopsis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D017124:Conserved Sequence; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: C556250:MIRN171 microRNA, Arabidopsis; D035683:MicroRNAs; D012322:RNA Precursors; D018749:RNA, Plant