Hepatic Lipid Accumulation Alters Global Histone H3 Lysine 9 and 4 Trimethylation in the Peroxisome Proliferator-Activated Receptor Alpha Network Hee-Jin Jun, Jinyoung Kim, Minh-Hien Hoang, Sung-Joon Lee* Department of Biotechnology, Graduate School of Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea Abstract Recent data suggest that the etiology of several metabolic diseases is closely associated with transcriptome alteration by aberrant histone methylation. We performed DNA microarray and ChIP-on-chip analyses to examine transcriptome profiling and trimethylation alterations to identify the genomic signature of nonalcoholic fatty liver disease (NAFLD), the most common form of chronic liver disease. Transcriptome analysis showed that steatotic livers in high-fat diet-fed apolipoprotein E2 mice significantly altered the expression of approximately 70% of total genes compared with normal diet-fed control livers, suggesting that hepatic lipid accumulation induces dramatic alterations in gene expression in vivo. Also, pathway analysis suggested that genes encoding chromatin-remodeling enzymes, such as jumonji C-domain- containing histone demethylases that regulate histone H3K9 and H3K4 trimethylation (H3K9me3, H3K4me3), were significantly altered in steatotic livers. Thus, we further investigated the global H3K9me3 and H3K4me3 status in lipid- accumulated mouse primary hepatocytes by ChIP-on-chip analysis. Results showed that hepatic lipid accumulation induced aberrant H3K9me3 and H3K4me3 status in peroxisome proliferator-activated receptor alpha and hepatic lipid catabolism network genes, reducing their mRNA expression compared with non-treated control hepatocytes. This study provides the first evidence that epigenetic regulation by H3K9me3 and H3K4me3 in hepatocytes may be involved in hepatic steatosis and the pathogenesis of NAFLD. Thus, control of H3K9me3 and H3K4me3 represents a potential novel NAFLD prevention and treatment strategy. Citation: Jun H-J, Kim J, Hoang M-H, Lee S-J (2012) Hepatic Lipid Accumulation Alters Global Histone H3 Lysine 9 and 4 Trimethylation in the Peroxisome Proliferator-Activated Receptor Alpha Network. PLoS ONE 7(9): e44345. doi:10.1371/journal.pone.0044345 Editor: Ingrid A. Dahlman, Karolinska Insitutet, Sweden Received January 30, 2012; Accepted August 2, 2012; Published September 4, 2012 Copyright: 2012 Jun et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was supported by the Technology Development Program for Fisheries of the Ministry for Food, Agriculture, Forestry and Fisheries, Republic of Korea (iPET, F20926409H220000110), and the Basic Science Research Program of the National Research Foundation of Korea (NRF), funded by the Ministry of Education, Science and Technology (20100028180). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: junelee@korea.ac.kr Introduction Histone methylation is one of the most important epigenetic mechanisms for transcriptional regulation of gene expression [1,2]. Lysine residues in histone proteins, such as H3K4, -9, -27, -36, - 79, and H4K20, are favorable sites for mono-, di-, and trimethylation (me1, me2, and me3, respectively) [3,4]. The degree of methylation at a specific Lys residue in a histone octamer influences the recruitment of effector proteins, thereby affecting chromatin structure and regulating the transcription of down- stream genes [5]. Histone methylation regulates a variety of nuclear processes essential for cellular regulation, homeostasis, and fate [5]. Thus, an aberrant histone methylation profile on a genome-wide scale has been associated with many human diseases, such as cancer, through controlling the transcription of down- stream target genes [6–8]. Nonalcoholic fatty liver disease (NAFLD) occurs in 10–24% of the general population in various countries [9]. Several lifestyle diseases, including metabolic syndrome, obesity, type 2 diabetes, arterial hypertension, and hyperlipidemia, have been shown to be associated with NAFLD [10,11]. However, the mechanisms involved in the development of NAFLD have not yet been fully clarified. Therefore, a better understanding of the biochemical and pathological changes during the development of NAFLD is needed. The prevalence of hyperlipidemia in patients with NAFLD is 20–92% [9]. Assy et al. reported that approximately half of patients with hyperlipidemia exhibited NAFLD upon ultrasound examination, and hypertriglyceridemia rather than hypercholesterolemia was associated with the risk of NAFLD [12]. Thus, in general, net retention of lipids within hepatocytes, mostly in the form of triglycerides, is a prerequisite for the development of NAFLD. Based on this evidence, NAFLD is characterized by the accumulation of triglyceride within hepatocytes. However, the primary metabolic abnormalities leading to lipid accumulation are not well understood. Recently, some studies have shown that epigenetic mechanisms are linked to metabolic disorders such as obesity, type II diabetes, hyperlipidemia, atherosclerosis, and cardiovascular disease [13,14]. Jumonji C-domain-containing histone demethylase 2A (JHDM2a) is an H3K9 demethylase that catalyzes the removal of H3K9 methylation. JHDM2a-knockout mice developed obesity, hypertriglyceridemia, hypercholesterolemia, hyperinsulinemia, and hyperleptinemia with increased body fat deposition and elevated serum lipid levels, regardless of age or food intake [13]. PLOS ONE | www.plosone.org 1 September 2012 | Volume 7 | Issue 9 | e44345