RT Journal Article
SR Electronic
T1 Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants
JF The Plant Cell
JO Plant Cell
FD American Society of Plant Biologists
SP 2398
OP 2416
DO 10.1105/tpc.16.00295
VO 28
IS 10
A1 Hou, Cheng‐Yu
A1 Lee, Wen‐Chi
A1 Chou, Hsiao‐Chun
A1 Chen, Ai‐Ping
A1 Chou, Shu‐Jen
A1 Chen, Ho‐Ming
YR 2016
UL http://www.plantcell.org/content/28/10/2398.abstract
AB 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.GlossaryXRNexoribonucleaseNMDnonsense-mediated mRNA decayPTCpremature termination codonORFopen reading frameUTRuntranslated regionuORFupstream open reading framemiRNAmicroRNAPAREparallel analysis of RNA ends5Pseq5′ P sequencingCDScoding sequenceCPuORFconserved peptide uORFAdoMetS-adenosyl-l-methioninetasiRNAtrans-acting siRNAGEOGene Expression Omnibus