Tissue-specificity of RNA editing in plant: analysis of transcripts from three tobacco (Nicotiana tabacum) varieties

RNA editing is a significant post-transcriptional molecular process of modifying the primary transcripts by editosome. In plants, it remains unknown whether and to what extent RNA editing contributes to tissue-specific regulation from a global perspective. To obtain an overview of RNA editing events in model plant tobacco (Nicotiana tabacum), we implemented a bioinformatics analysis of DNA-Seq and RNA-Seq data from roots and leaves of three tobacco varieties (TN90, Basma and K326). The results showed that hundreds of RNA editing sites were detected to be located in the protein-coding region of plastid/mitochondria for all three varieties. Among these sites, some of them were detected in leaves but not or reduced in roots. Interestingly, most of the disappeared editing sites in roots were located in plastid transcripts encoding subunits of NADH dehydrogenase. The average editing efficiencies in roots were reduced significantly compared with leaves across three varieties in both organelles. In addition, we found that the reduction of RNA editing efficiency in mitochondria is mild compared with plastid. Expression analysis further showed that an extraordinarily high percentage of RNA editing factors were down-regulated in roots, particularly for PPR, MORF proteins, indicating that the distinct editing patterns between roots and leaves might result from the differential regulation of RNA editing factors expression. This study provides references and insights into understanding the function of plant RNA editing in tissue-specific regulation mediated by editosomes.