Early Moderate Prenatal Alcohol Exposure and Maternal Diet Impact Offspring DNA Methylation Across Species
Alcohol consumption in pregnancy can affect genome regulation in the developing offspring but results have been contradictory. We employed a physiologically relevant murine model of short-term moderate prenatal alcohol exposure (PAE) resembling common patterns of alcohol consumption in pregnancy in humans. Early moderate PAE was sufficient to affect site-specific DNA methylation in new-born pups without altering behavioural outcomes in adult littermates. Whole-genome bisulfite sequencing of neonatal brain and liver revealed stochastic influence on DNA methylation that was mostly tissue-specific, with some perturbations likely originating as early as gastrulation. DNA methylation differences were enriched in non-coding genomic regions with regulatory potential indicative of broad effects of alcohol on genome regulation. Replication studies in human cohorts with fetal alcohol spectrum disorder suggested some effects were metastable at genes linked to disease-relevant traits including facial morphology, intelligence, educational attainment, autism, and schizophrenia. In our murine model, a maternal diet high in folate and choline protected against some of the damaging effects of early moderate PAE on DNA methylation. Our studies demonstrate that early moderate exposure is sufficient to affect fetal genome regulation even in the absence of overt phenotypic changes and highlight a role for preventative maternal dietary interventions. Overall design: To investigate the effects of early moderate prenatal alcohol exposure in mice and the effect of a high methyl donor diet, we designed an experiment with four treatment arms: prenatal alcohol exposure-normal chow, prenatal alcohol exposure-high methyl donor diet, water-normal chow and water-high methyl donor diet.    We conducted whole-genome bisulfite sequencing on newborn mouse brain and liver, selecting two males and two females  from each group (n = 16). We used human datasets generated from Illumina Human Methylation EPIC array to validate observations from the murine model.