Abstract
BackgroundC-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.ResultsBy 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.ConclusionsThe 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.
Highlights
C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants
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
We find that the 5-prime nucleotide and the RNA secondary structures affect C-to-U RNA editing in cis, and transcription factors might affect editing in trans
Summary
C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. 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. 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 generation sequencing (NGS) technique. Chu and Wei BMC Genetics (2020) 21:98 Despite these fruitful findings in functional RNA editing and the convenience for accessing the editing sites, it remains uninvestigated that, at genome-wide level, what are the cis and trans determinants affecting the occurrence or editing levels of these C-to-U events? Other determinants especially the cis-regulatory elements remain largely undiscovered
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