Genome-Wide Profiling of Histone H3 Lysine 4 and Lysine 27 Trimethylation Reveals an Epigenetic Signature in Prostate Carcinogenesis

et al. (2009) Genome-Wide Profiling of Histone H3 Lysine 4 and Lysine 27 Trimethylation Reveals an Epigenetic Signature in Prostate Carcinogenesis. PLoS ONE 4(3): e4687. doi:10.1371/journal.pone.0004687 Genome-Wide Profiling of Histone H3 Lysine 4 and Lysine 27 Trimethylation Reveals an Epigenetic Signature in Prostate Carcinogenesis Xi-Song Ke 0 Yi Qu 0 Kari Rostad 0 Wen-Cheng Li 0 Biaoyang Lin 0 Ole Johan Halvorsen 0 Svein A. 0 Haukaas 0 Inge Jonassen 0 Kjell Petersen 0 Naomi Goldfinger 0 Varda Rotter 0 Lars A. Akslen 0 Anne M. Oyan 0 Karl-Henning Kalland 0 Mikhail V. Blagosklonny, Ordway Research Institute, United States of America 0 1 The Gade Institute, University of Bergen , Bergen , Norway , 2 Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , People's Republic of China, 3 Swedish Medical Center , Seattle , Washington, United States of America, 4 Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University , Hangzhou , People's Republic of China, 5 Department of Pathology, Haukeland University Hospital , Bergen , Norway , 6 Department of Surgical Sciences, University of Bergen , Bergen , Norway , 7 Department of Surgery, Haukeland University Hospital , Bergen , Norway , 8 Computational Biology Unit, Bergen Center for Computational Science, University of Bergen , Bergen , Norway , 9 Department of Informatics, University of Bergen , Bergen , Norway , 10 Department of Molecular Cell Biology, Weizmann Institute of Science , Rehovot , Israel , 11 Department of Microbiology and Immunology, Haukeland University Hospital , Bergen , Norway Background: Increasing evidence implicates the critical roles of epigenetic regulation in cancer. Very recent reports indicate that global gene silencing in cancer is associated with specific epigenetic modifications. However, the relationship between epigenetic switches and more dynamic patterns of gene activation and repression has remained largely unknown. Methodology/Principal Findings: Genome-wide profiling of the trimethylation of histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) was performed using chromatin immunoprecipitation coupled with whole genome promoter microarray (ChIP-chip) techniques. Comparison of the ChIP-chip data and microarray gene expression data revealed that loss and/or gain of H3K4me3 and/or H3K27me3 were strongly associated with differential gene expression, including microRNA expression, between prostate cancer and primary cells. The most common switches were gain or loss of H3K27me3 coupled with low effect on gene expression. The least prevalent switches were between H3K4me3 and H3K27me3 coupled with much higher fractions of activated and silenced genes. Promoter patterns of H3K4me3 and H3K27me3 corresponded strongly with coordinated expression changes of regulatory gene modules, such as HOX and microRNA genes, and structural gene modules, such as desmosome and gap junction genes. A number of epigenetically switched oncogenes and tumor suppressor genes were found overexpressed and underexpressed accordingly in prostate cancer cells. Conclusions/Significance: This work offers a dynamic picture of epigenetic switches in carcinogenesis and contributes to an overall understanding of coordinated regulation of gene expression in cancer. Our data indicate an H3K4me3/H3K27me3 epigenetic signature of prostate carcinogenesis. - Funding: This work was supported by Helse Vest (grants no. 911005, 911227 and 911401), the Research Council of Norway (grants. no. 154942/310, 163920/V50 and 185676/V40) and The Norwegian Cancer Society (grants no. HS01-2006-0446, HS01-2006-0468, HS02-2008-0188), the European Commission 6th Framework Program Contract 504743 and the UroBergen Research Fund. 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. Epigenetics refers to heritable, but potentially reversible, alternated phenotypic states without difference in genotype. The proteins that mediate epigenetic changes are involved in dynamic transcriptional control of gene expression and are encoded by more than 100 genes including DNA methyltransferases (DNMTs), histone acetyltransferases (HATs), histone deacetylases (HDACs), histone methyltransferases (HMTs), histone demethylases (HDMTs) and chromatin remodelling enzymes [1]. EZH2 (Enhancer of Zeste homolog 2), a known core component of the polycomb repressive complex 2 (PRC2), is one of the best characterized HMTs, and can trimethylate the histone H3 lysine 27 (H3K27) and thereby repress gene transcription [2]. Previous work has shown that EZH2 was significantly upregulated and associated with high proliferation rate and aggressive tumor subgroups in prostate cancer [3]. However, the targets and output of epigenetic regulation in prostate cancer are still not completely understood. Genome-wide profiling of the H3K27me3 modification in prostate cancer has been carried out by a few groups. Yu et al. have analyzed H3K27me3 location and suggested a polycomb repression signature in metastatic prostate cancer [4]. It would be informative if H3K27me3 locations were also mapped in benign tissues to show the cancer specificity of the signature. Very recently, H3K27me3 modifications were mapped in both prostate cancer and normal cell lines and a set of genes silenced by EZH2mediated H3K27 trimethylation specifically in prostate cancer was identified [5]. Both works shed light on the silencing function of EZH2 in prostate cancer, but little is known about epigenetic gene activation in prostate carcinogenesis. To systematically examine the role of epigenetic regulation in prostate cancer, we have screened dysregulated genes in prostate cancer tissues and cell lines using microarray techniques. We found that the most significantly changed epigenetic regulators in both prostate cancer tissues and cell lines were EZH2, SMYD3 and DNMT3A, which function as H3K27 trimethyltransferase, H3K4 di/tri-methyltransferase [6] and DNA methyltransferase [7], respectively. Trimethylation of H3K27 (H3K27me3) and trimethylation of H3K4 (H3K4me3) are associated with repression and activation of gene transcription, respectively [2,6]. To examine the hypothesis that dysregulated genes in prostate cancer contain a distinct pattern of H3K4me3 and H3K27me3, ChIPchip analysis was performed for genome-wide profiling of H3K4me3 and H3K27me3 modification patterns in both prostate primary cells and cancer cells. Comparison of the epigenetic switches and gene expression switches between normal primary and cancer cells indicated an H3K4me3/H3K27me3 epigenetic signature in prostate carcinogenesis. Dysregulated Epigenetic Genes in Prostate Cancer To analyze the dysregulated epigenetic genes in prostate cancer, we screened the microarray gene expression data of prostate can (...truncated)