The 579-bp structural variant in PIK3C3 regulates gene expression and modulates immune responses in Xiang pigs.

Abstract

Structural variants (SVs) are a type of mutations in animal genomes that have shown their role in the process of domestication. An insertion/ deletion of 579 bp SV in intron 21 of PIK3C3 gene in Xiang pigs was detected by genome resequencing method in our previous study. Phosphoinositide-3-kinase, class III (PIK3C3), is a critical regulator of autophagy, essential for cellular homeostasis, pathogen clearance, and immune modulation. The aim of this study was to investigate the polymorphism of intron 21 of the PIK3C3 gene of Xiang pigs and its effect on PIK3C3 expression. The polymorphism of SV PIK3C3-579 was determined by PCR. Three genotypes of this SV were detected in different breeds with uneven distribution among them. Two Short interspersed elements (SINEs) located in the SV region, opposite in the direction of PIK3C3 gene. RT-qPCR revealed that the SINE insertion significantly decreased PIK3C3 expression in the spleen of Xiang pigs and was associated with the production of the PIK3C3-circRNA. The fluorescent reporter assays confirmed that the SINE insertion significantly decreased the activity of the EGFP promoter. Additionally, The SINE deletion was associated with elevated levels of lymphocyte, monocyte, neutrophil, IFN-γ and IL-2. These data suggested that the SINE insertion could regulate the expression of PIK3C3 gene and the biogenesis of circular RNA, thereby modulating the immune response of Xiang pigs, which provides insights into the functional impact of structural variants on immune traits in this breed.