Pan YX. High-fat diet caused widespread epigenomic differences on hepatic methylome in rat. Physiol Genomics 47: 514 -523, 2015. First published July 21, 2015; doi:10.1152/physiolgenomics.00110.2014.-A high-fat (HF) diet is associated with progression of liver diseases. To illustrate genome-wide landscape of DNA methylation in liver of rats fed either a control or HF diet, two enrichment-based methods, namely methyl-DNA immunoprecipitation assay with high-throughput sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq), were performed in our study. Rats fed with the HF diet exhibited an increased body weight and liver fat accumulation compared with that of the control group when they were 12 wk of age. Genome-wide analysis of differentially methylated regions (DMRs) showed that 12,494 DMRs induced by HF diet were hypomethylated and 6,404 were hypermethylated. DMRs with gene annotations [differentially methylated genes (DMGs)] were further analyzed to show gene-specific methylation profile. There were 88, 2,680, and 95 hypomethylated DMGs identified with changes in DNA methylation in the promoter, intragenic and downstream regions, respectively, compared with fewer hypermethylated DMGs (45, 1,623, and 50 in the respective regions). Some of these genes also contained an ACGT cis-acting motif whose DNA methylation status may affect gene expression. Pathway analysis showed that these DMGs were involved in critical hepatic signaling networks related to hepatic development. Therefore, HF diet had global impacts on DNA methylation profile in the liver of rats, leading to differential expression of genes in hepatic pathways that may involve in functional changes in liver development. DMR; DNA hypomethylation; gene expression; high-fat diet; MeDIP THE INTERACTION BETWEEN NUTRITIONAL and epigenetic influences on the gene regulation is of great interest to researchers (27). For decades, due to the limitation and cost of the experimental technology for detecting DNA methylation (6), most studies focused on how diet affects the promoter methylation profile of a single gene and its relationship with gene expression. Recent advancements in sequencing-based DNA methylation profiling methods including methyl-DNA immunoprecipitation assay in combination with high-throughput sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq) have allowed researchers to map out DNA methylation profile in a genome-wide fashion (30).Consumption of a high-fat (HF) diet may cause numerous health consequences, including extensive hepatic triglyceride accumulation, insulin resistance, oxidative damage, and chronic low-grade inflammation, which leads to progression of liver diseases and fibrosis (2,8,34). Metabolism and cell cycle-related genes in liver tissue are known to be subject to regulation by DNA methylation. For instance, methylation intensity at specific CpG sites on Esr1 (7) and stearoyl-CoA desaturase 1 (Scd1) (29), glucokinase, pyruvate kinase (18), and MTTP (4) genes ...