Quantifying the genome-wide functional consequences of DNA methylation associated with early life adversity. - PROJECT SUMMARY
People that experience adversity during early life exhibit increased risk for a number of health disorders
throughout the lifespan. For example, adverse childhood experiences predict elevated susceptibility to anxiety
disorders in adulthood, increased stress reactivity, and altered immune function. However, the physiological
and molecular mechanisms that connect early life experiences to health outcomes later in life remain poorly
understood. Further, not everyone experiences the same consequences, suggesting that later life environment
or genetic variation may exacerbate, or protect against, the negative consequences of early life insults.
The biological embedding of early life experiences is thought to arise, at least in part, from persistent
changes to the epigenome in response to early life conditions. DNA methylation (the addition of a methyl group
to cytosine bases), has received particular attention in this regard, because DNA methylation marks can be
highly stable and can influence gene regulation. In support of this idea, DNA methylation levels at thousands of
genomic regions have now been associated with early life adversity. However, if these changes explain
variation in human health, differential methylation at these sites must also have functional consequences for
gene regulation—an assumption that is rarely empirically tested. Characterizing the subset of cases in which
early adversity-associated DNA methylation variation can influence downstream traits is therefore a central
priority for understanding the role of epigenetics in the health consequences of early life adversity.
To address this priority, the proposed study will perform the first comprehensive test of the functional
consequences of early life adversity-associated DNA methylation variation for gene regulation. Specifically, it
will use a novel, high-throughput method (mSTARR-seq) to test whether DNA methylation marks alter gene
regulatory activity at 10,000 candidate regions in the human genome. Because DNA methylation may be
differentially important across cell types, this relationship will be investigated in three cell types with known
links to the biology of early life adversity: immune cells in the blood, neural cells, and adrenocortical cells that
are important in the stress response. In addition, because the effects of early adversity-associated DNA
methylation may depend on genotype or other environmental stressors, we will test for methylation-dependent
regulatory activity across genetically variable humans and under environmental challenges. Finally, we will use
CRISPR-dCas9 epigenome editing to investigate whether precisely altered DNA methylation levels change
gene regulation of individual genes. At its conclusion, the proposed work will generate the first systematic
assessment of the regulatory consequences of early adversity-associated DNA methylation. Its findings will
therefore provide much-needed insight into the key targets of early life adversity in the epigenome, with the
goal of identifying new opportunities for treatment and intervention.
