RNA editing is a post-transcriptional process leading to differences between genomic DNA and transcript sequences, potentially enhancing transcriptome diversity. With recent advances in high-throughput sequencing, many efforts have been made to describe mRNA editing at the transcriptome scale, especially in mammals, raising contradictory conclusions regarding the extent of this phenomenon. We show by a detailed description of the 25 studies focusing so far on mRNA editing at the whole-transcriptome scale that systematic sequencing artifacts are somehow considered in most studies, whereas biological replication is often neglected and multi-alignment not properly evaluated, which ultimately impairs the legitimacy of results. We recently developed a rigorous strategy to identify mRNA editing using mRNA and genomic DNA sequencings, taking into account sequencing and mapping artifacts, and biological replicates. We applied this method to screen for mRNA editing in liver and white adipose tissue from 8 chickens and confirm the small extent of mRNA recoding in this species. Among the 25 unique edited sites identified, 3 events were previously described in mammals, attesting this phenomenon is conserved through evolution. Deeper investigations on 5 sites revealed the impact of tissular context, genotype, age, feeding condition and sex on mRNA editing levels. More specifically, this analysis highlighted that the editing level at the site located on COG3 was strongly regulated by 4 out of these factors. By comprehensively characterizing the mRNA editing landscape in chicken, our results highlight how this phenomenon is limited, and suggest a regulation of editing levels by various genetic and environmental factors.
- Received September 4, 2015.
- Accepted November 26, 2015.
- Copyright © 2015 Author et al.
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