SINE Insertion in the Intron of Pig May Decrease Its Expression by Acting as a Repressor.

The genetic diversity of the axis genes and their association with the variation of gene expression and phenotypic traits, principally represented by SNPs, have been extensively reported. Nevertheless, the impact of retrotransposon insertion polymorphisms (RIPs) on the axis gene activity has not been reported. In the present study, bioinformatic prediction and PCR verification were performed to screen RIPs in four axis genes (, , and ). In total, five RIPs, including one SINE RIP in intron 3 of , one L1 RIP in intron 7 of , and three SINE RIPs in intron 1, intron 5 and intron 9 of , were confirmed by PCR, displaying polymorphisms in diverse breeds. Dual luciferase reporter assay revealed that the SINE insertion in intron 1 of significantly repressed the promoter activity in PK15, Hela, C2C12 and 3T3-L1 cells. Furthermore, qPCR results confirmed that this SINE insertion was associated with a decreased expression of in the leg muscle and longissimus dorsi, indicating that it may act as a repressor involved in the regulation of expression. In summary, our data revealed that RIPs contribute to the genetic variation of axis genes, whereby one SINE RIP in the intron 1 of may decrease the expression of by acting as a repressor.