Epstein-Barr virus (EBV) isMethylation of genomic DNA is observed in many species across the phylogenic spectrum, from unicellular prokaryotes to humans. While the principal function of methylation of bacterial genomes has been determined to be protection of self DNA from cleavage by endogenous restriction endonucleases (which act to prevent the acquisition of foreign DNA sequences), most evidence suggests that the primary function of genome methylation in higher eukaryotes (i.e., vertebrates) is the regulation of gene expression. Numerous studies over the past two decades have demonstrated a repressive effect of cytosinemethylated CpG dinucleotides in promoter sequences on gene expression. Thus, cytosine methylation has been widely regarded as a general mechanism by which eukaryotic promoters can be inactivated, perhaps by effecting changes in chromatin structure which make methylated promoters inaccessible to the transcriptional apparatus (reviewed in references 3 and 57). That the inactivity of hypermethylated loci is an effect, rather than a cause, of DNA methylation has been demonstrated by characterization of transgenic mice in which methylation of genomic DNA was impaired or eliminated via targeted disruption of the endogenous methyltransferase gene. In embryos derived from the methyltransferase-deficient mice, a strong correlation was observed between the absence of methylation and activated transcription of the characteristically hypermethylated and silent allele of certain (imprinted) genes (42).Since methylation appears to play a role in the regulation of endogenous gene expression, it is reasonable to expect that promoter usage of at least some eukaryotic viruses may also be regulated by host cell methyltransferase activity. CpG methylation is believed to silence transcription from integrated retroviral genomes until later cellular events (e.g., cellular differentiation) trigger demethylation and reactivation of the retroviral genome (3,19,25,26). Additionally, analyses of gene expression from integrated adenovirus genomes have demonstrated a strong correlation between CpG methylation of specific adenovirus promoters and silenced transcription from the corresponding viral genes (37, 39). Several other examples of repression of viral gene expression by host-cell-determined methylation of viral DNA sequences have been reported; these include Marek's disease virus (20, 31), simian foamy virus type 3 (72), and Epstein-Barr virus (EBV) (see below).Several different groups have contributed to a detailed analysis of EBV genome methylation (1,10,27,45,49,58,67). These studies have revealed that whereas the EBV genome is nearly free of CpG methylation in lymphoblastoid cell lines (LCLs) established by in vitro infection of B cells (type III latency), the genome is heavily CpG methylated in the subset of Burkitt's lymphoma (BL) tumor cell lines which retain the phenotype of the freshly explanted tumor (type I latency). There is thus a correlation between heavy methylation of the EBV genome and restricted expre...