title: Are ta-siRNAs only originated from the cleavage site of miRNA on its target RNAs and phased in 21-nt increments?
abstract: Trans-acting siRNAs (ta-siRNAs) are a class of small RNAs playing crucial roles in the regulation of plant gene expression. According to the canonical model, specific miRNA-guided cleavage of a TAS transcript triggers and sets the registry for the subsequent production of ta-siRNAs at 21-nt increments from the cleavage site. However, a previously validated 22-nt ta-siR2140 indicated that ta-siRNAs might be initiated from other phase increments and registers, which resulted in massive ta-siRNAs missing in the canonical model. To test this hypothesis, we employed high-throughput sequencing data to thoroughly identify the miR173-triggered ta-siRNAs from TAS1/TAS2 transcripts. As a result, thousands of phased siRNAs not generated through the canonical pathway were identified and 110 novel siRNA-target interactions were further validated based on degradome sequencing data. Based on these results, we propose that the canonical biogenesis model of ta-siRNAs should be modified in order to recruit the previously unidentified ta-siRNA candidates.
authors.affiliation: College of Life Sciences, Huzhou University, Huzhou 313000, PR China.
authors.forename: Lan
authors.initials: L
authors.lastname: Yu
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China. Electronic address: mengyijun@zju.edu.cn.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Meng
authors.affiliation: College of Life Sciences, Huzhou University, Huzhou 313000, PR China. Electronic address: shaocg@hutc.zj.cn.
authors.forename: Chaogang
authors.initials: C
authors.lastname: Shao
authors.affiliation: Agronomy and Plant Breeding Department, Razi University, Kermanshah, Iran; Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
authors.forename: Danial
authors.initials: D
authors.lastname: Kahrizi
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D048749:Cytokinesis; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering
keywords: Arabidopsis; Biogenesis; Gene regulatory networks; MicroRNAs; RNA; Small interfering