Investigating a personalised nutrition approach for modulating epigenetic profiles using over-expressed DNMTs in cell lines

Abstract

DNA methylation is an epigenetic mechanism that enables heritable changes in gene expression without changes in DNA sequence. Methyl groups are transferred from the methyl donor S-adenosyl methionine (SAM) to the 5-carbon of cytosine by DNA methyltransferases (DNMTs). The DNMT family comprises a set of DNA-modifying enzymes and uses a similar catalytic mechanism to form a covalent reaction intermediate between the substrate base and the enzyme. Food-derived bioactive compounds are among the exogenous factors that can modulate the DNA methylation patterns, either via generating SAM through one-carbon metabolism or by inhibiting the activity of DNMTs. In this study, cell lines with stable over-expression of each of 13 DNMTs isoform (DNMT3A1, DNMT3A2, DNMT3B1, DNMT3B2, DNMT3B3, DNMT3B4, DNMT3B5, DNMTΔ3B1, DNMTΔ3B2, DNMTΔ3B3, DNMTΔ3B4, DNMT3L, and DNMT1) were generated by lentiviral transduction of human embryonic kidney cells (HEK293T). DNA methylation patterns in these 13 cell lines were analysed by Illumina Infinium Methylation EPIC BeadChip, which interrogates more than 850,000 CpG sites across the genome. The sensitivity and specificity of each DNMT isoform to selected food constituents (caffeic acid (CA), (-)-Epigallocatechin-3-gallate (EGCG), curcumin, vitamin C, and theaflavin) were investigated by quantification of DNA methylation at specific CpG sites targeted by the DNMTs, using pyrosequencing. DNA methylation patterns for each DNMT isoform were obtained and the potential underlying biological mechanisms for DNMT-target CpGs were explored. At the selected CpG sites, DNA methylation was decreased with CA and vitamin C in DNMT∆3B4 and DNMT3A2 cells, respectively. In addition, the enzymatic activity of DNMT∆3B4 decreased after CA treatment. In summary, despite similarity of their protein structures, DNMT isoforms show regional specificity in the maintenance of DNA methylation patterns. This study also revealed that the activity of DNMT∆3B4 and DNMT3A2 can be specifically modulated by CA and vitamin C, respectively, in a dose-response manner. These observations further understanding of nutrition-epigenetic mechanisms, especially interactions with enzymatic activity, could be applied to modulate DNA methylation profiles using food-derived bioactive compounds in personalised nutrition.