Evidence of RNA Editing in Pig Longissimus Dorsi Muscle

RNA editing refers to post-transcriptional modifications of RNA transcripts, most thought to be catalyzed by adenosine deaminase acting on RNA. This substitutes adenosine for inosine in a site-specific and tissue-dependent manner, observed as an adenosine to guanine edit of RNA with respect to DNA in next-gen sequencing studies. Our objective was to use next-gen sequencing to identify potential RNA editing sites in pigs. We used genomic DNA and longissimus dorsi (LD) muscle RNA from an F2 pig from our Duroc-Pietrain population. Non-strand specific polyA RNAseq data from LD was used to call candidate RNA editing sites. Whole genome sequence was used to call genotypes. DNAseq and RNAseq reads were aligned to SScrofa 10.2 using bowtie2 and tophat. Only high quality bases (Phred Score>25) from uniquely mapped reads were used. Candidate editing sites had homozygous genotypes in DNAseq data, with a sequencing depth of at least 10 reads. Evidence for a possible editing event required five or more RNAseq reads with alternative alleles. A total of 686 candidate RNA editing sites were observed with A to G being the most common. Sites were found across all autosomes and the X chromosome, with the majority located in upstream and downstream gene proximal regions, intronic variants and UTRs. Results indicate the overall composition of transcriptome-wide RNA editing in swine resembles other studies in primates. Future efforts are warranted to identify RNA editing events in additional pig tissues, as well as determine impacts of RNA editing on transcriptional regulation and important phenotypes.