Funata Sayaka, Matsusaka Keisuke, Yamanaka Ryota, Yamamoto Shogo, Okabe Atsushi, Fukuyo Masaki, Aburatani Hiroyuki, Fukayama Masashi, Kaneda Atsushi
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.
Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Oncotarget. 2017 Jul 21;8(33):55265-55279. doi: 10.18632/oncotarget.19423. eCollection 2017 Aug 15.
Aberrant DNA hypermethylation is a major epigenetic mechanism to inactivate tumor suppressor genes in cancer. Epstein-Barr virus positive gastric cancer is the most frequently hypermethylated tumor among human malignancies. Herein, we performed comprehensive analysis of epigenomic alteration during EBV infection, by Infinium HumanMethylation 450K BeadChip for DNA methylation and ChIP-sequencing for histone modification alteration during EBV infection into gastric cancer cell line MKN7. Among 7,775 genes with increased DNA methylation in promoter regions, roughly half were "DNA methylation-sensitive" genes, which acquired DNA methylation in the whole promoter regions and thus were repressed. These included anti-oncogenic genes, e.g. . The other half were "DNA methylation-resistant" genes, where DNA methylation is acquired in the surrounding of promoter regions, but unmethylated status is protected in the vicinity of transcription start site. These genes thereby retained gene expression, and included DNA repair genes. Histone modification was altered dynamically and coordinately with DNA methylation alteration. DNA methylation-sensitive genes significantly correlated with loss of H3K27me3 pre-marks or decrease of active histone marks, H3K4me3 and H3K27ac. Apoptosis-related genes were significantly enriched in these epigenetically repressed genes. Gain of active histone marks significantly correlated with DNA methylation-resistant genes. Genes related to mitotic cell cycle and DNA repair were significantly enriched in these epigenetically activated genes. Our data show that orchestrated epigenetic alterations are important in gene regulation during EBV infection, and histone modification status in promoter regions significantly associated with acquisition of DNA methylation or protection of unmethylated status at transcription start site.
异常的DNA高甲基化是癌症中使肿瘤抑制基因失活的主要表观遗传机制。爱泼斯坦-巴尔病毒（EBV）阳性胃癌是人类恶性肿瘤中甲基化最频繁的肿瘤。在此，我们通过Infinium HumanMethylation 450K BeadChip进行DNA甲基化分析以及通过ChIP测序分析EBV感染胃癌细胞系MKN7过程中的组蛋白修饰变化，对EBV感染期间的表观基因组改变进行了全面分析。在启动子区域DNA甲基化增加的7775个基因中，约一半是“DNA甲基化敏感”基因，这些基因在整个启动子区域获得DNA甲基化并因此被抑制。这些基因包括抗癌基因，例如 。另一半是“DNA甲基化抗性”基因，其在启动子区域周围获得DNA甲基化，但转录起始位点附近的未甲基化状态受到保护。这些基因因此保留了基因表达，其中包括DNA修复基因。组蛋白修饰与DNA甲基化改变动态且协同地发生变化。DNA甲基化敏感基因与H3K27me3预标记的缺失或活性组蛋白标记H3K4me3和H3K27ac的减少显著相关。凋亡相关基因在这些表观遗传抑制的基因中显著富集。活性组蛋白标记的增加与DNA甲基化抗性基因显著相关。与有丝分裂细胞周期和DNA修复相关的基因在这些表观遗传激活的基因中显著富集。我们的数据表明，精心编排的表观遗传改变在EBV感染期间的基因调控中很重要，并且启动子区域的组蛋白修饰状态与DNA甲基化的获得或转录起始位点未甲基化状态的保护显著相关。
