Large-scale potential RNA editing profiling in different adult chicken tissues.

Abstract

RNA editing is a post-transcription maturation process that diversifies genomically encoded information and can lead to transcriptome diversity. Thanks to next-generation sequencing technologies, a large number of editing sites have been identified in different species. Although this mechanism is well described in mammals, only a few studies have been performed in chicken. Here, candidate or potential RNA editing sites were identified in eight different tissues of chicken (brain, spleen, colon, lung, kidney, heart, testes and liver). We identified 68 A-to-G editing sites in 46 genes. Only two of these were previously reported in chicken. We found no C-to-T sites, attesting to the lack of this type of editing mechanism in chicken. Similar to mammals, the editing sites were enriched in non-coding regions, rarely resulted in a change in amino acids, showed a critical role in the nervous system and had a low guanosine level upstream of the editing site and some enrichment downstream from the site. Moreover, in contrast to mammals, editing sites were weakly enriched in interspersed repeats and the number and editing ratio of non-synonymous sites were higher than for those of synonymous sites. Interestingly, we found several tissue-specific edited genes, including GABRA3, SORL1 and HTR1D in brain and RYR2 and FHOD3 in heart, that were associated with functional processes relevant to the corresponding tissue. This finding highlights the importance of RNA editing in several chicken tissues, especially the brain, and establishes a foundation for further exploration of this process.