Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana.

Ruchika Ruchika,Matomo Sakari,Toshifumi Tsukahara,Chisato Okudaira

doi:10.3390/cells10030635

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, pentatricopeptide 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 presence 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.

Highlights

RNA editing, one of the most promising means of post-transcriptional gene regulation, has been widely investigated in various protozoa [1], mammalian apolipoprotein-B [2], animals [3], fungi [4], bacteria [5,6], and viruses [7,8] as well as in plants [9,10,11]
(Inosine) RNA editing is observed in animal nuclear genes, while C-to-U RNA editing is not limited to animals but is spreading in plant organelles
In RNA sequencing (RNA-seq) analysis, gene expression level is estimated by counting the number of reads mapped onto genes or exons

Summary

Introduction

RNA editing, one of the most promising means of post-transcriptional gene regulation, has been widely investigated in various protozoa [1], mammalian apolipoprotein-B [2], animals [3], fungi [4], bacteria [5,6], and viruses [7,8] as well as in plants [9,10,11]. The mechanism of cytidine-touridine (C-to-U) RNA editing in plant organelles is completely different from that in animal nucleus and reasonably well understood, mainly owing to the characterization of many. The RNA editing machinery, collectively described as the editosome, consists of at least four proteins including pentatricopeptide repeat (PPR). Direct selection of target sites is governed by PLS subclass PPR proteins with additional E1 and E2 domains only or further C-terminal DYW domain, which is most likely to catalyze C to

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Results

Conclusion