An introduction to EpiPol (Epigenetic affecting Polymorphism) concept with an in silico identification of CpG-affecting SNPs in the upstream regulatory sequences of human AHR gene

Abstract

DNA methylation, histone modification, and ncRNA function are the main epigenetic mechanisms involved in the regulation of gene expression and there are single nucleotide polymorphisms (SNPs) that may affect them. Although these SNPs have an important role in connecting genetic and epigenetic levels of gene regulation, they have not been classified in an independent category until now. Therefore, we introduce the EpiPol concept, which abbreviates the epigenetic affecting polymorphism and describes those variations in the regulatory sequences of a gene, which may affect epigenetic regulations of its expression. Aryl hydrocarbon receptor (AHR) is a multifunctional regulator in cell physiology and xenobiotics metabolism and its altered regulation have been shown to result in adverse developmental and physiological outcomes. Recently, the therapeutic potential of modulating the methylation status of the AHR promoter has been discussed. Using Bioinformatics approaches, we aimed to identify the polymorphisms in upstream regulatory sequences of AHR, which may affect the epigenetic regulation of it through the introduction or removal of CpG dinucleotides that act as possible targets for DNA methylation. The 3000 bp upstream regulatory sequences of AHR, −2700 to +300 relative to the ATG codon, were obtained from NCBI. The CpG-island identified and all 105 SNPs located in it were retrieved from dbSNP. After that, 45 SNPs that cause the introduction or removal of CpGs were identified as candidate EpiPols of AHR. Then, the methylation status of these EpiPols analyzed using Bioinformatics servers, and finally, 13 SNPs were reported as predicted methylation-affecting EpiPols of the human AHR gene.