Characterization of RNA editing on porcine NR3C1, COG3, and ACSM2B genes

The RNA-Seq technology is largely used in quantitative gene expression studies, but the use of RNA-Seq technology allows also for detecting differential allelic expression and posttranscriptional modifications such as RNA-editing. RNA-editing is a posttranscriptional mechanism that generates new transcripts from a limited gene number in the genome, and consists in the chemical alteration of nucleotide bases of RNA molecules. In the present study, we have characterized RNA-editing patterns in six porcine tissues: hypothalamus, liver, diaphragm, Longissimus dorsi, cardiac muscles, and backfat of three genes suffering of these posttranscriptional modifications. In a previous RNA-Seq assay conducted on hepatic and hypothalamus tissues from nine Iberian x Landrace backcrossed pigs, over 90,000 SNPs were discovered and annotated. Among them, three SNPs on NRSC1 (ENSSSCG00000014401g.102797T > C), COG3 (ENSSSCG00000027815g.4525A > G) and ACSM2B (ENSSSCG00000007858g.13374T > A) genes revealed different genotype conditional on analyzed tissue. The validation through Sanger sequencing on gDNA and cDNA revealed unexpected genotypes. Some transcripts showed alleles that are not present in the corresponding gDNA sequence, supporting the hypothesis of RNA-editing modifications. These results were also validated by pyrosequencing on gDNA and cDNA and on different set of samples and tissues from Iberian and Iberian x Large White pigs. The COG3gA525A > G modification has been previously described in several species, proving that at least some RNA-editing conservation happens across vertebrate species. The modification on the COGS transcript, key molecule in protein metabolism, changes the Isoleucine amino acid to Valine at protein position 83. Besides, it lies in an exon enhancer region involved in the promotion of alternative splicing, which is likely linked to different biological functions conditional on tissue. The NR3C1g.102797T > C and ACSM2Bg.13374A > T modifications have not been previously described. The modification on NR3C1 lies in the 3'UTR region, likely located in a potential miRNA target site. Finally, the modification on ACSM2B produces an amino acid change from Serine to Treonine at position 272. This change lies in a splicing site, and more importantly, it can be considered of major interest because the different hepatic transcripts showed interindividual variations that could be functionally related to the phenotypic traits. The RNA-editing patterns obser