The ability of environmental factors to shape health and disease involves epigenetic mechanisms that mediate gene-environment interactions. To study environmental influences on the fetal epigenome, we utilized the viable yellow agouti (A^vy) mouse, in which coat color variation is correlated to epigenetic marks established early in development. Maternal dietary supplementation with genistein, the major phytoestrogen in soy, shifted the coat color of A^vy/a offspring toward pseudoagouti (brown) by increasing A^vy CpG methylation. Hypermethylation persisted into adulthood and protected offspring from obesity. Second, maternal dietary exposure to bisphenol A (BPA), an estrogenic plasticizer, shifted the coat color of A^vy/a offspring toward yellow by decreasing A^vy methylation. CpG methylation was also decreased at another metastable locus, the CDK5 activator binding protein (Cabp^IAP). In both studies, A^vy methylation was similar in tissues from the three germ layers, indicating that genistein and BPA act early in development. Third, maternal dietary nutritional supplementation with either methyl donors or genistein negated the hypomethylating effects of this plasticizer on the epigenome of the offspring, showing that simple dietary changes can protect against the deleterious effects of environmental toxicants on the fetal epigenome.

Metastable epialleles are alleles that are variably expressed in genetically identical individuals due to epigenetic modifications established during early development. Herein, we report the first characterization of histone modifications within the A^vy metastable epiallele. Yellow mice, which are hypomethylated at A^vy, also display enrichment of activating histone acetylation modifications. Pseudoagouti mice, in which A^vy hypermethylation is thought to silence ectopic expression, exhibit enrichment of H4K20 methylation, indicating that DNA methylation acts in concert with histone modifications to affect variable metastable epiallele expression. To characterize additional metastable epialleles within the mouse genome, we utilized genome-wide expression arrays and identified several candidate genes displaying the 'Agouti Expression Fingerprint,' defined as large variability in gene expression among individuals concomitant with a low variability in gene expression among tissues in the three germ layers. The elucidation of the epigenetic basis of gene-environment interactions as well as the genome-wide identification of metastable epialleles will strengthen human health risk assessment and shape diagnostic and therapeutic strategies for disease.