GSE59842
Genome wide DNA methylation of Epstein-Barr virus infected immortalized normal oral keratinocytes
The oral cavity is the persistent reservoir for EBV with lifelong infection of resident epithelial and B cells. Infection of these cell types results in distinct EBV gene expression patterns that are regulated by epigenetic modifications involving DNA methylation and chromatin structure. Such regulation of EBV gene expression relies on viral manipulation of the host epigenetic machinery that may inadvertently result in long-lasting, oncogenic host epigenetic reprogramming. To test this hypothesis in the context of EBV infection of epithelial cells, we established a transient infection model to identify the epigenetic consequences after EBV infection of immortalized normal oral keratinocytes and subsequent viral loss. Overall design: NOK cells were single cell cloned (designated as cl1) and EBV infected by co-culture with a recombinant Akata EBV strain carrying neomcycin resistance and GFP expression cassette in place of EBV BXLF1.  Cells were selected with 350 ug/ml G418.  As a selection control, cells were transfected a plasmid carrying a neomycin resistance cassette.  Cells were passaged 10 times with G418, followed by removal of selection pressure.  After an additional 10 passages, cells were single cell cloned and the presence of EBV was determined by various methods.  Three clones were identified as being EBV negative and said to be transiently infected.  Uninfected parental and vector transfected cells were passaged in the same manner and also single cell cloned.    The DNA methylation profiles were examined using reduced representation bisulfite sequencing.