Impact of the 294 bp SINE Insertion in 5′UTR of the GLYATL3 Gene on Gene Expression and Phenotypic Variation

SINEs are one type of the most frequently found DNA repetitive sequences in the eukaryotic genome. The polymorphism generated by SINE insertion may affect proximal host genes and even cause phenotypic variations in domestic animals. Glycine N-acyltransferase-like 3 (<i>GLYATL3</i>) is a member of the N-acyltransferase family which may play a role in amino acid and fatty acid metabolism. Previous studies have identified short interspersed nuclear element (SINE) insertion sites in the 5'UTR region of <i>GLYATL3</i>. This study investigated the effects of the 294 bp SINE insertion on <i>GLYATL3</i> expression and phenotypic variation. The polymerase chain reaction (PCR) was used to determine the distribution of <i>GLYATL3</i>-SINE-RIP in 15 pig breeds. SINE insertions were absent in hybrid pigs and present in all purebred pigs. Correlation analysis further revealed significant differences in SINE+/+ and SINE-/- individuals when they reached 30 kg of body weight. In light of these findings, qPCR revealed that the SINE insertion significantly increased <i>GLYATL3</i> expression in the cerebellum of Mi pigs. Additionally, dual-luciferase reporter assays confirmed that the SINE insertion significantly enhanced the activity of the Oct4 promoter. Preliminary evidence indicates the SINE insertion may modulate an increase in the growth rate of pigs through transcriptional regulation of <i>GLYATL3</i>. As a new type marker, this SINE-insertion polymorphism may assist genetic selection to optimize growth traits in porcine breeding programs.