Functional analysis of 3’UTR polymorphisms in the caprine SLC11A1 gene and its association with the Mycobacterium avium subsp. paratuberculosis infection

•SLC11A1 gene of goat activity variation is associated with specific nature of the stimulus.•The A16-B8 genotype is the most prominent, with the strongest transcriptional effect of 3′UTR.•The A16-B8 genotype was found to be more responsive to MAP exposure.•Within the genomic region of SLC11A1 gene were detected different functional regulatory elements.•85 putative miRNAs were detected to be localized externally or between polymorphic regions A and B. The study aimed to investigate whether the genetic polymorphisms in the 3′UTR of the caprine SLC11A1 gene are functional, and to assess the role of MAP as a regulatory parameter in gene expression. To this goal we constructed plasmids expressing the Luciferase reporter gene in transient transfections of a mouse (Balb/c) macrophage cell line (RAW264.7), incorporating those polymorphisms that our previous work indicated as more prominent in terms of SLC11A1 expression and responsiveness to MAP infection. Gene expression variation was recorded on the average of the respective measurements after exposure to Mycobacterium avium subsp. paratuberculosis (MAP) combined with microbial antigens and cytokines. In silico analysis of the region under study allowed identification of one cis-acting RNA element, five putative transcriptional regulatory elements and 85 3’end microRNA binding sites. The two polymorphic regions (regions A and B) of the 3’UTR of the caprine SLC11A1 gene were recognized as regulators of its activity, at transcriptional and post-transcriptional level. The GT16 polymorphism at region A, combined with the GT8 polymorphism at region B, results in up-regulation of the SLC11A1 gene. The specific genotype was also found to be more responsive to MAP exposure at a statistically significant level.