title: Cascading cis-cleavage on transcript from trans-acting siRNA-producing locus 3.
abstract: The production of small RNAs (sRNAs) from phased positions set by microRNA-directed cleavage of trans-acting-siRNA-producing locus (TAS) transcript has been characterized extensively; however, the production of sRNAs from non-phased positions remains unknown. We report three cis-cleavages that occurred in TAS3 transcripts in Vitis vinifera, by combining high-throughput sRNA deep sequencing information with evolutional conservation and genome-wide RNA degradome analysis. The three cis-cleavages can be deciphered to generate an orderly cleavage cascade, and can also produce distinct phasing patterns. Each of the patterns, either upstream or downstream of the cis-cleaved position, had a set of sRNAs arranged in 21-nucleotide increments. Part of the cascading cis-cleavages was also conserved in Arabidopsis thaliana. Our results will enhance the understanding of the production of sRNAs from non-phased positions that are not set by microRNA-directed cleavage.
authors.affiliation: College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China. zhang_chq2002@sohu.com
authors.forename: Changqing
authors.initials: C
authors.lastname: Zhang
authors.forename: Guangping
authors.initials: G
authors.lastname: Li
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
authors.forename: Shinong
authors.initials: S
authors.lastname: Zhu
authors.forename: Hailing
authors.initials: H
authors.lastname: Li
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D053837:DNA Cleavage; D056426:Genetic Loci; D018745:Genome, Plant; D035683:MicroRNAs / Q000378:metabolism; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000378:metabolism*; D027843:Vitis / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering