Nutr Res Pract.  2017 Apr;11(2):105-113. 10.4162/nrp.2017.11.2.105.

Genome-wide hepatic DNA methylation changes in high-fat diet-induced obese mice

• Yoon A
• Tammen SA
• Park S
• Han SN
• Choi SW

• KMID: 2412022
• DOI: http://doi.org/10.4162/nrp.2017.11.2.105

Abstract

BACKGROUND/OBJECTIVES
A high-fat diet (HFD) induces obesity, which is a major risk factor for cardiovascular disease and cancer, while a calorie-restricted diet can extend life span by reducing the risk of these diseases. It is known that health effects of diet are partially conveyed through epigenetic mechanism including DNA methylation. In this study, we investigated the genome-wide hepatic DNA methylation to identify the epigenetic effects of HFD-induced obesity.
MATERIALS AND METHODS
Seven-week-old male C57BL/6 mice were fed control diet (CD), calorie-restricted control diet (CRCD), or HFD for 16 weeks (after one week of acclimation to the control diet). Food intake, body weight, and liver weight were measured. Hepatic triacylglycerol and cholesterol levels were determined using enzymatic colorimetric methods. Changes in genome-wide DNA methylation were determined by a DNA methylation microarray method combined with methylated DNA immunoprecipitation. The level of transcription of individual genes was measured by real-time PCR.
RESULTS
The DNA methylation statuses of genes in biological networks related to lipid metabolism and hepatic steatosis were influenced by HFD-induced obesity. In HFD group, a proinflammatory Casp1 (Caspase 1) gene had hypomethylated CpG sites at the 1.5-kb upstream region of its transcription start site (TSS), and its mRNA level was higher compared with that in CD group. Additionally, an energy metabolism-associated gene Ndufb9 (NADH dehydrogenase 1 beta subcomplex 9) in HFD group had hypermethylated CpG sites at the 2.6-kb downstream region of its TSS, and its mRNA level was lower compared with that in CRCD group.
CONCLUSIONS
HFD alters DNA methylation profiles in genes associated with liver lipid metabolism and hepatic steatosis. The methylation statuses of Casp1 and Ndufb9 were particularly influenced by the HFD. The expression of these genes in HFD differed significantly compared with CD and CRCD, respectively, suggesting that the expressions of Casp1 and Ndufb9 in liver were regulated by their methylation statuses.

Keyword

DNA methylation; obesity; liver; Caspase 1; NADH dehydrogenase

MeSH Terms

Acclimatization
Animals
Body Weight
Cardiovascular Diseases
Caspase 1
Cholesterol
Diet
Diet, High-Fat
DNA Methylation*
DNA*
Eating
Epigenomics
Humans
Immunoprecipitation
Lipid Metabolism
Liver
Male
Methods
Methylation
Mice
Mice, Obese*
NADH Dehydrogenase
Obesity
Oxidoreductases
Real-Time Polymerase Chain Reaction
Risk Factors
RNA, Messenger
Transcription Initiation Site
Triglycerides
Caspase 1
Cholesterol
DNA
NADH Dehydrogenase
Oxidoreductases
RNA, Messenger
Triglycerides

Figure

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  Fig. 1 Heat maps showing differentially methylated probes in each comparison. (A) CD vs. CRCD comparison. (B) HFD vs. CD comparison. (C) HFD vs. CRCD comparison. CRCD, calorie-restricted control diet; CD, control diet; HFD, high-fat diet.

• 

  Fig. 2 Distance between DMRs and their annotated genes. The number of DMRs falling within the designated intervals relative to their annotated genes' transcription start sites (TSSs) are presented above each bar. This graph was generated via Stanford University's GREAT Analysis. DMRs: differentially methylated regions.

• 

  Fig. 3 Network 1 of the HFD vs. CD comparison. This network is involved in gastrointestinal disease, hepatic system disease, and liver steatosis. Red: Genes found in our data that were hypomethylated in HFD group. Green: Genes found in our data that were hypermethylated in HFD group. HFD, high-fat diet; CD, control diet.

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  Fig. 4 Relative level of Casp1 mRNA in the HFD group compared with that of the CD group. The value are expressed as means ± SEM, n = 7 for each group. Student's t-test P-value is shown. HFD, high-fat diet; CD, control diet.

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  Fig. 5 Network 1 of the HFD vs. CRCD comparison. This network is involved in lipid metabolism, molecular transport, and small molecule biochemistry. Red: Genes found in our data that were hypomethylated in HFD group. Green: Genes found in our data that were hypermethylated in HFD group. HFD, high-fat diet; CRCD, calorie-restricted control diet.

• 

  Fig. 6 Relative level of Ndufb9 mRNA inthe HFD group compared with that of the CRCD group. The values are expressed as means ± SEM, n = 6 for CRCD and 7 for HFD. Student's t-test P-value is shown. HFD, high-fat diet; CRCD, calorie-restricted control diet.

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