Dynamic landscape of mitochondrial Cytidine-to-Uridine RNA editing in tobacco (Nicotiana tabacum) shows its tissue specificity

Zhiyu Deng,Aidi Zhang,Xiujun Zhang,Tengfei Wang,Xiaohan Jiang,Jing Fang

doi:10.1007/s11240-021-02194-0

Abstract

RNA editing is a prevalent nucleotide modification at the RNA level in higher plants. However, little is known about the dynamic distribution of RNA editing among tissues. In this study, we explored the tissue specificity of mitochondrial RNA editing in tobacco (Nicotiana tabacum) based on publicly available RNA-seq data from four tobacco tissues: root, stem, leaf, and flower. As a result, 473 RNA editing sites involved in 60 mitochondrial genes were identified. The results showed an uneven distribution of editing sites among tobacco tissues, a total of 106 sites and 11 genes were identified as tissue-specific editing in the four tissues, and a total of 11 sites located in six genes were detected differentially edited statistically (p-value < 0.01). The expression of RNA edited genes and RNA editing factors was analyzed, and we observed that most tissue-specific edited genes were expressed at a low level. There were about ~ 20 RNA editing factors that were differentially expressed between different tissues, indicating that the heterogeneity of RNA editing in different tissues might result from the expression regulation of RNA editing factors. Our analyses provide insights into the understanding of landscape, regulation, and function of RNA editing events in higher plants.

Highlights

RNA editing is defined as the insertion, deletion, and replacement of nucleotide bases that occurs after transcription, which usually results in difference between RNA genetic information and the genome template (Liscovitch-Brauer et al, 2017; Walkley and Li, 2017; Zahn, 2017; Peng et al, 2018)
A total of 331 RNA editing sites involving in 54 mitochondrial genes were identified
The result shows that the expression level of Pentapeptide repeat protein (PPR) genes in each tissue varies from different tissues, indicating the heterogeneity of RNA editing in different tissues might result from the tissue specificity of PPR genes expression

Summary

Introduction

RNA editing is defined as the insertion, deletion, and replacement of nucleotide bases that occurs after transcription, which usually results in difference between RNA genetic information and the genome template (Liscovitch-Brauer et al, 2017; Walkley and Li, 2017; Zahn, 2017; Peng et al, 2018). In 1986, Dutch etbiologist Benne et al discovered an RNA editing event in the mitochondrial gene cytochrome c oxidase subunit II (cox2) of trypanosomes firstly (Benne et al, 1986), they found that the insertion of four uridines caused the cox gene to form a continuous open reading frame, resulting in changes in genetic information. More and more RNA editing events were confirmed. RNA editing has been found in primitive eukaryotes, vertebrates, plants, fungi and viruses (Palladino et al, 2000; Bahn et al, 2012; Alon et al, 2015; Guo et al, 2015; Riemondy et al, 2018; Zaidan et al, 2018)

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Conclusion