A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript

Abstract

In our previous study, we identified a Short Interspersed Nuclear Element Retrotransposon Insertion Polymorphism (SINE-RIP) within the 3' untranslated region (3'UTR) of the Phospholipase A2 Group XVI (PLA2G16) gene, which is essential in lipid metabolism. In this study, we confirmed the presence of this 280 bp SINE insertion and examined its distribution across ten distinct pig breeds using PCR and sequencing. Subsequently, RT-PCR was employed to determine its potential for co-transcription. Finally, qPCR analysis was performed to evaluate the insertion's effect on PLA2G16 expression. The results indicated significant polymorphism at this site among different breeds. The SINE insertion can co-transcribe with PLA2G16 and shows a tissue-specific relationship with its expression in backfat and liver. Specifically, in Sujiang and Mi pigs, individuals homozygous for the SINE insertion (SINE^+/+) demonstrated significantly lower PLA2G16 expression (p < 0.01) in backfat compared to those without the insertion (SINE^-/-). Conversely, in Sujiang pigs, SINE^+/+ individuals exhibited significantly higher expression (p < 0.05) in the liver compared to SINE^-/- counterparts. These findings suggest that the SINE insertion in the 3'UTR of PLA2G16 can fuse with the target gene, forming a new transcript that may affect gene expression levels in a tissue-specific manner.

Keywords: SINE; 3′UTR; Fusion transcripts; PLA2G16.