Acute enterovirus infections significantly alter host cellular DNA methylation status

Acute infections with enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) usually cause Hand, foot and mouth disease (HFMD) among infants and young children with several large outbreaks worldwide. Unfortunately, the molecular mechanisms underlying enterovirus infections remain largely unknown. In this study, we analyzed the genome-wide DNA methylation patterns of host cells in response to EV71 and CVA16 infections using the Illumina Infinium HumanMethylation450 BeadChip. Of over 480,000 loci studied, significant differential methylation was observed between EV71 infected-cells and control cells at 3957 CpG sites, out of which 2478 were hypermethylated and 1479 were hypomethylated, whereas CVA16 infection resulted in methylation level changes of 5194 CpG sites with 4288 hypermethylated and 906 hypomethylated. These differential methylated loci displayed a wide range of genomic distributions in chromosomes, inside and surrounding areas (shores and shelves) of CpG islands, as well as functional gene regions including promoter, gene body and 3'UTR. Based on methylation alterations, 1189 genes were identified to be potentially co-associated with the replication processes of two enteroviruses. GO function annotation and enrichment analysis of 1189 common differentially methylated genes reflected a broad spectrum of biological regulatory events during viral infection. KEGG pathway analysis indicated the involvement of diverse signaling pathways including viral myocarditis, Notch signaling and antigen processing and presentation. Our present study provides a novel insight into enterovirus-host interaction network at epigenetic profile, thus contributing to improved understanding of HFMD pathogenesis.