Elsevier

Molecular Metabolism

Volume 6, Issue 4, April 2017, Pages 327-339
Molecular Metabolism

Original Article
DNA methylation alters transcriptional rates of differentially expressed genes and contributes to pathophysiology in mice fed a high fat diet

https://doi.org/10.1016/j.molmet.2017.02.001Get rights and content
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open access

Highlights

  • Mice placed on a 14-week high fat diet displayed genes that were hypermethylated and underexpressed compared to controls.

  • Chromatin immunoprecipitation demonstrated decreased RNA pol II phosphorylation on Phlda1 and Onecut1 in the high fat fed mice, consistent with decreased transcriptional rates.

  • A subnetwork of genes downstream of Phlda1, involved in lipid homeostasis, were suppressed both by a high fat diet and by knockdown of Phlda1 in vivo using an adenovirus-delivered shRNA.

  • Knock-down of Phlda1 presented with increased lipid droplet sizes, consistent with the global Phlda1 knockout mouse model, which displays liver steatosis on a standard chow diet.

  • We conclude that a high fat diet is sufficient to alter DNA methylation in adults and contributes to the pathophysiology of obesity.

Abstract

Objective

Overnutrition can alter gene expression patterns through epigenetic mechanisms that may persist through generations. However, it is less clear if overnutrition, for example a high fat diet, modifies epigenetic control of gene expression in adults, or by what molecular mechanisms, or if such mechanisms contribute to the pathology of the metabolic syndrome. Here we test the hypothesis that a high fat diet alters hepatic DNA methylation, transcription and gene expression patterns, and explore the contribution of such changes to the pathophysiology of obesity.

Methods

RNA-seq and targeted high-throughput bisulfite DNA sequencing were used to undertake a systematic analysis of the hepatic response to a high fat diet. RT-PCR, chromatin immunoprecipitation and in vivo knockdown of an identified driver gene, Phlda1, were used to validate the results.

Results

A high fat diet resulted in the hypermethylation and decreased transcription and expression of Phlda1 and several other genes. A subnetwork of genes associated with Phlda1 was identified from an existing Bayesian gene network that contained numerous hepatic regulatory genes involved in lipid and body weight homeostasis. Hepatic-specific depletion of Phlda1 in mice decreased expression of the genes in the subnetwork, and led to increased oil droplet size in standard chow-fed mice, an early indicator of steatosis, validating the contribution of this gene to the phenotype.

Conclusions

We conclude that a high fat diet alters the epigenetics and transcriptional activity of key hepatic genes controlling lipid homeostasis, contributing to the pathophysiology of obesity.

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Keywords

DNA methylation
RNA-seq
Transcription
High fat diet
Liver
Phlda1

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Current address: Pediatric Cardiology, Morgan Stanley Children's Hospital, Columbia University Medical Center of New York Presbyterian, USA.