title: Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants.
abstract: High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 5'-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). Based on this analysis, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nucleotide periodicity in the position of free 5' RNA ends and a bias toward the translational frame. By examining conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice, we found a predominance of 5' termini of RNA degradation intermediates that were separated by a length equal to a ribosome-protected mRNA fragment. Through the analysis of RNA degradome data, we discovered uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, our analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a noncleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling.
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Cheng-Yu
authors.identifier: 0000-0003-4195-9165
authors.initials: CY
authors.lastname: Hou
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Lee
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.|Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan.
authors.forename: Hsiao-Chun
authors.initials: HC
authors.lastname: Chou
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Ai-Ping
authors.initials: AP
authors.lastname: Chen
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan.
authors.forename: Shu-Jen
authors.initials: SJ
authors.lastname: Chou
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan homing@gate.sinica.edu.tw.
authors.forename: Ho-Ming
authors.identifier: 0000-0001-5979-0121
authors.initials: HM
authors.lastname: Chen
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D035683:MicroRNAs / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000378:metabolism*; D018749:RNA, Plant / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods; D013025:Glycine max / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant