Date of Award

Summer 8-15-2017

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Evolution, Ecology & Population Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



As obesity rates continue rising nationally and globally, it is crucial to understand how a high-fat diet disrupts the regulation of the genome and leads to adverse health effects. Uncovering the underlying gene expression and DNA methylation changes induced by an individual’s high-fat diet and a maternal high-fat diet can pinpoint new targets for epigenetic therapies and reveal the physiological and behavioral changes in obesity. The goal of this dissertation is to gain deeper insight into the DNA methylation and gene expression changes that occur in response to a high-fat diet.

I studied the response to dietary fat within two generations of the inbred SM/J mouse strain by feeding them either a low-fat diet or a high-fat diet that was nearly isocaloric but had approximately three times as many calories from fat. I measured their weights weekly for 17 weeks, tested their glucose and insulin tolerance, assessed serum biomarkers, and weighed their organs at necropsy. Diet strongly affected all of these traits. I isolated RNA from the liver tissue and used RNA-sequencing to uncover 4,356 genes that were differentially expressed due to diet. Nearly 200 of these genes had a significant sex-by-diet interaction, highlighting the importance of sex differences in the response to a high-fat diet. The dysregulated genes were enriched for pathways involved in cytokine-cytokine receptor interaction, chemokine signaling, and oxidative phosphorylation. I extracted DNA from the liver tissue and identified differentially methylated regions across the genome using MeDIP and MRE sequencing. More than 7,000 genes in the liver had differentially methylated regions at the FDR-adjusted q < 0.05 level. The differentially methylated regions occurred in differentially expressed genes significantly more often than expected by chance alone. These findings underscore the major effect that dietary fat has on gene expression and DNA methylation patterns in the liver, and illustrate how different this effect is depending on sex.

I then mated low-fat-fed males with females on either diet, and cross-fostered all offspring to low-fat-fed SM/J nurses in order to study the effect of prenatal maternal diet on adult offspring metabolic traits, behavior, gene expression, and DNA methylation. I weaned the offspring onto a high fat or low-fat diet at 3 weeks of age. I then measured the same traits in the offspring as I measured in the parental generation, as well as additional morphological and behavioral traits. I measured the long-bone lengths and weights, anxiety with the Open Field Test, behavior with instantaneous scan sampling, and nest quality with the Deacon Scale. Compared to low-fat-fed offspring, high-fat-fed offspring had longer, heavier bones, had increased anxiety levels, built lower-quality nests, and had reduced activity levels in adulthood, including exploratory and self-maintenance behaviors. Maternal diet did not have much of an impact on offspring bones or behavior, only affecting whether or not the offspring built their nests inside a hut.

Although maternal diet did not widely affect offspring behavior, it had major effects on the obesity and diabetes-related traits in the adult daughters. Compared to high-fat-fed daughters of low fat mothers, high-fat-fed daughters of high-fat mothers weighed more, had heavier livers and reproductive fat pads, and had higher leptin levels in their serum. These physiological changes were accompanied by 46 differentially expressed genes and 1,700 differentially methylated genomic regions in liver cells, as well as 45 differentially expressed genes and 4,103 differentially methylated genomic regions in heart cells. Although the obesity traits were only altered by maternal diet only in the daughters, all offspring experienced changes in the expression of dozens of genes in the liver, particularly genes involved in RNA processing, immune response, and cellular respiration in mitochondria. Maternal obesity also altered DNA methylation in thousands of regions in the genome. Over 7,300 genes contained at least one differentially methylated region due to maternal diet in high-fat-fed offspring, and over 9,300 genes did in low-fat-fed offspring. Regardless of maternal diet, an offspring high-fat diet reduced overall variation in methylation, increased body size—as measured by the weights of the organs and body, and the weights and lengths of the long bones—decreased insulin sensitivity, and altered the expression of 3,908 genes. While the mice were more affected by their own individual diets, their maternal diet impacted their DNA methylation and gene expression into adulthood. The findings of this dissertation improve our understanding of the epigenetic architecture of obesity and identify new targets for therapies in the future.


English (en)

Chair and Committee

James Cheverud

Committee Members

Ken Olsen, Jenny Duncan, Allan Larson, Ting Wang,


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