Genome-Wide DNA Methylation Profiling in Dietary Intervention Studies: a User’s Perspective

Abstract

Within the past decade, epigenetic mechanisms and their modulation by dietary agents have gained major interest in the cancer prevention and nutrition community. Gene expression is epigenetically regulated by DNA methylation, histone tail modifications, and non-coding (micro) RNAs. Given the fact that epigenetic aberrations are reversible and represent potentially initiating events in the development of diseases, they have been identified as promising new targets for prevention strategies. Evidence is accumulating that dietary cancer chemopreventive agents from various sources, including green tea, soy, turmeric, broccoli, and other fruit and vegetables, can modulate DNA methylation, at least in vitro. To facilitate in vivo studies with focus on genome-wide modulation of DNA methylation, we here give an overview on current affinity enrichment- and bisulfite treatment-based methodologies for methylation profiling that might be useful for rodent models and human intervention studies. We also summarize genome-wide methylome analyses performed with dietary agents in vitro and in vivo and conclude with some practical considerations for the design of future dietary intervention studies.