Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana
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RESEARCH ARTICLE
Open Access
Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana Duan Chu and Lai Wei*
Abstract Background: C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The biological functions of a fraction of C-to-U editing sites are continuously discovered by case studies. However, at genome-wide level, the cis and trans determinants affecting the occurrence or editing levels of these C-to-U events are relatively less studied. What is known is that the PPR (pentatricopeptide repeat) proteins are the main trans-regulatory elements responsible for the C-to-U conversion, but other determinants especially the cis-regulatory elements remain largely uninvestigated. Results: By analyzing the transcriptome and translatome data in Arabidopsis thaliana roots and shoots, combined with RNA-seq data from hybrids of Arabidopsis thaliana and Arabidopsis lyrata, we perform genome-wide investigation on the cis elements and trans-regulatory elements that potentially affect C-to-U editing events. An upstream guanosine or double-stranded RNA (dsRNA) regions are unfavorable for editing events. Meanwhile, many genes including the transcription factors may indirectly play regulatory roles in trans. Conclusions: The 5-prime thymidine facilitates editing and dsRNA structures prevent editing in cis. Many transcription factors affect editing in trans. Although the detailed molecular mechanisms underlying the cis and trans regulation remain to be experimentally verified, our findings provide novel aspects in studying the botanical C-to-U RNA editing events. Keywords: C-to-U RNA editing, Cis, Trans, Regulatory, Arabidopsis, Synonyms“Missense” and “nonsynonymous”.
Key message In Arabidopsis thaliana, the 5-prime nucleotide and the RNA secondary structures affect C-to-U RNA editing in cis while many transcription factors play regulatory roles in trans. Background In the plant kingdom, C-to-U RNA editing is one of the most prevalent RNA modifications and is enriched in the chloroplast and mitochondrial genes [1–6]. The biological functions of particular C-to-U editing events are discovered [7–10]. For example, phenotypic studies have associated * Correspondence: [email protected] College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China
mitochondrial C-to-U editing with seed development in maize (Zea mays) and rice (Oryza sativa) [11–13]. Mechanistic study found that a particular C-to-U editing site in Oenothera gene nad1 is required for proper splicing of premRNA [14]. Early studies in sugar beet (Beta vulgaris) and tobacco (Nicotiana tabacum) found that mitochondrial Cto-U editing events were able to create translation start codons and produce functionally important proteins [15–17]. Apart from these case studies on editing function, the large-scale identification of C-to-U editing sites appeared in recent years with the development of next generation sequencing (NGS) technique. Bioinformat
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