Epigenomic aberration by episomal binding of Epstein-Barr virus genome in nasopharyngeal carcinoma

Abstract

Gene expression in cancer is regulated by genomic aberrations, such as gene mutations and copy number abnormalities, as well as epigenomic aberrations, such as DNA methylation, histone modifications, and chromatin conformation changes. Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignant epithelial tumor; however, its epigenomic aberrations have not been completely elucidated. We conducted comprehensive analyses of epigenomes in NPC by circular chromosome conformation capture sequencing (4C-seq), high-throughput chromosome conformation capture sequencing (Hi-C), chromatin immunoprecipitation sequencing (ChIP-seq), and ribonucleic acid sequencing (RNA-seq). In the genome of EBV (+) NPC cells (C666-1), 50 regions were present, where the EBV genome interacted (EBV-interacting regions, EBVIRs); they were significantly AT-rich and gene-poor compared with other regions. Hi-C analysis revealed that more than 90% of EBVIRs were repressed compartments in normal epithelial cells (NP69T), which suggested that they were heterochromatin regions. ChIP-seq showed low signals of active histone marks, including H3K27ac and H3K4me1, in NP69T cells; however, these increased in C666-1 cells, indicating aberrant activation of enhancers that promote gene expression. Within the EBVIR-overlapping topologically associating domains, 14 H3K4me3(+) genes were significantly upregulated in C666-1 cells. One of the target genes, PLA2G4A, interacted with enhancers activated in EBVIRs and was highly expressed in NPC; its knockdown significantly reduced cell proliferation. These results suggest that the EBV genome contributes to the carcinogenesis of NPC by activating enhancers within the suppressed heterochromatin in host cells.