Oncotarget

Research Papers:

TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection

Hiroe Namba-Fukuyo _, Sayaka Funata, Keisuke Matsusaka, Masaki Fukuyo, Bahityar Rahmutulla, Yasunobu Mano, Masashi Fukayama, Hiroyuki Aburatani, Atsushi Kaneda

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Oncotarget. 2016; 7:81512-81526. https://doi.org/10.18632/oncotarget.13130

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Abstract

Hiroe Namba-Fukuyo1,2,3, Sayaka Funata1,4, Keisuke Matsusaka1, Masaki Fukuyo1, Bahityar Rahmutulla1, Yasunobu Mano1, Masashi Fukayama4, Hiroyuki Aburatani5, Atsushi Kaneda1

1Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Japan

2Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan

3Japan Society for the Promotion of Science, Japan

4Department of Pathology, Graduate School of Medicine, The University of Tokyo, Japan

5Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Japan

Correspondence to:

Atsushi Kaneda, email: kaneda@chiba-u.jp

Keywords: DNA hydroxymethylation, DNA methylation, Epstein-Barr virus, gastric cancer, TET2

Received: August 01, 2016    Accepted: October 17, 2016    Published: November 05, 2016

ABSTRACT

Extensive DNA methylation is observed in gastric cancer with Epstein-Barr virus (EBV) infection, and EBV infection is the cause to induce this extensive hypermethylaton phenotype in gastric epithelial cells. However, some 5′ regions of genes do not undergo de novo methylation, despite the induction of methylation in surrounding regions, suggesting the existence of a resistance factor against DNA methylation acquisition. We conducted an RNA-seq analysis of gastric epithelial cells with and without EBV infection and found that TET family genes, especially TET2, were repressed by EBV infection at both mRNA and protein levels. TET2 was found to be downregulated by EBV transcripts, e.g. BARF0 and LMP2A, and also by seven human miRNAs targeting TET2, e.g., miR-93 and miR-29a, which were upregulated by EBV infection, and transfection of which into gastric cells repressed TET2. Hydroxymethylation target genes by TET2 were detected by hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq) with and without TET2 overexpression, and overlapped significantly with methylation target genes in EBV-infected cells. When TET2 was knocked down by shRNA, EBV infection induced de novo methylation more severely, including even higher methylation in methylation-acquired promoters or de novo methylation acquisition in methylation-protected promoters, leading to gene repression. TET2 knockdown alone without EBV infection did not induce de novo DNA methylation. These data suggested that TET2 functions as a resistance factor against DNA methylation in gastric epithelial cells and repression of TET2 contributes to DNA methylation acquisition during EBV infection.


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