Arabidopsis thaliana Raw sequence reads

High-throughput approaches for profiling the 5'' ends of RNA degradation intermediates on a genome-wide scale are frequently applied in the validation of cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome beyond miRNA targets currently is largely unclear which limits the application of degradome. We provide multiple lines of evidence to show that ribosome footprints are widespread in the plant degradome. A 3-nt periodicity and a bias toward the translational frame were observed in the analysis of 5' truncated mRNA ends mapped to the coding sequence (CDS). In addition, predominant 5' termini of RNA degradation intermediates separated by a length equal to a ribosome-protected fragment were evident in the conserved peptide upstream open reading frames (uORFs). Through the analysis of degradome data, we uncovered novel ribosome stalling uORFs including a lineage specific uORF in the Brassicaceae family. Phased degradation signatures of stacked ribosomes were also identified in the CDS of multiple genes. Furthermore, we show that the binding of ARGONAUTE7 to a non-cleavable target site of miR390 might directly hinder ribosome movement. This work shows that the RNA degradome contains in vivo ribosome-protected mRNA fragments and demonstrates an alternative use of degradome data in the study of ribosome stalling.

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