Genome‐wide identification of u‐to‐c rna editing events for nuclear genes in arabidopsis thaliana

Abstract

Cytosine‐to‐Uridine (C‐to‐U) RNA editing involves the deamination phenomenon, which is observed in animal nucleus and plant organelles; however, it has been considered the U‐to‐C is confined to the organelles of limited non‐angiosperm plant species. Although previous RNA‐seq-based analysis implied U‐to‐C RNA editing events in plant nuclear genes, it has not been broadly accepted due to inadequate confirmatory analyses. Here we examined the U‐to‐C RNA editing in Arabidopsis tissues at different developmental stages of growth. In this study, the high‐throughput RNA sequencing (RNA‐seq) of 12‐day‐old and 20‐day‐old Arabidopsis seedlings was performed, which enabled transcriptome‐wide identification of RNA editing sites to analyze differentially expressed genes (DEGs) and nucleotide base conversions. The results showed that DEGs were expressed to higher levels in 12‐day‐old seedlings than in 20‐day‐old seedlings. Additionally, penta-tricopeptide repeat (PPR) genes were also expressed at higher levels, as indicated by the log2FC values. RNA‐seq analysis of 12‐day‐ and 20‐day‐old Arabidopsis seedlings revealed candidates of U‐to‐C RNA editing events. Sanger sequencing of both DNA and cDNA for all candidate nucleotide conversions confirmed the seven U‐to‐C RNA editing sites. This work clearly demonstrated pres-ence of U‐to‐C RNA editing for nuclear genes in Arabidopsis, which provides the basis to study the mechanism as well as the functions of the unique post‐transcriptional modification.