The Effect of the Microbiome on DNA Methylation

Abstract

DNA methylation is an epigenetic mark with profound impact on gene expression and regulation. It is known to be altered both in cancer and throughout aging. These aging and cancer related changes are characterized by hyper-methylation of normally unmethylated CpG islands, and global DNA hypomethylation. Microbiota-free mice are known to live longer than their normal counterparts, and microbial dysbiosis is known to be a hallmark of colorectal cancer. In order to determine the microbiota’s ability to impact DNA methylation patterns, that in turn may influence aging phenotypes and cancer development, the DNA methylomes of germ-free (GF; no microbiome) and specific pathogen free (SPF; controlled microbiome) mice were analyzed with a DREAM assay. This was done in wild-type mice and in IL-10 KO mice, with or without the addition of the colitis-associated cancer inducing compound, azoxymethane (AOM). We found that individually, inflammation and the microbiota induce moderate changes in the methylation profiles of the large intestine. However, their effects on DNA methylation seem to synergize; in the presence of inflammation, SPF mice have highly different methylation profiles than GF mice. In addition, inflammation causes large methylation changes in specific-pathogen-free mice, but only moderate changes in germ-free mice. The inflammation and microbiota induced changes were characterized by hyper-methylation of sites with low methylation (CpG islands), and hypomethylation of sites with high methylation; these patterns resembled the DNA methylation drift seen during aging and in transformed cells. All sites subject to age-related methylation drift were vulnerable to the microbiome, but the converse was not true. A subset of sites was vulnerable to only the microbiome/inflammation, indicating multiple mechanisms of action. Overall, this research indicates the microbiota plays a key role in determining host DNA methylation state.