GLOBAL CpG METHYLATION ANALYSIS OF THE HUMAN GENOME REVEALS MAJOR HYPO AND HYPER METHYLATION IN KAPOSI’S SARCOMA ASSOCIATED HERPESVIRUS INFECTED CELLS

Kaposi’s sarcoma associated herpesvirus (KSHV, HHV-8) is the etiological agent of Kaposi’s sarcoma (KS), and is tightly associated with primary effusion lymphoma (PEL) and multicentric Castleman’s disease (MCD). The association of KS with immunosuppression such as AIDS makes it the most common malignancy in Africa today. Following infection, the virus establishes a latency program that enables the virus to remain in the infected host for life, and latency is the major phase in herpes-virus associated malignancies. Previously, we have shown that KSHV latency protein LANA, leads to CpG DNA methylation of certain host cell promoters by interacting with the cellular de-novo DNA methyltransferase DNMT3a. In an attempt to fully understand the epigenetic impact of KSHV latency on disease progression and development, we performed a genome wide CpG methylation analysis on several uninfected and KSHV-infected cells including KSHV-associated malignancies. We have identified a panel of hyper-methylated cellular promoters in KSHV infected cells, and gene expression analysis confirmed their transcription repression in KSHV-associated malignancies. Surprisingly, on top of these newly methylated sites, our analysis revealed a major differential genome wide hypo-methylation of up to 25% of the genome in KSHV infected cells. Interestingly, the patterns of CpG hypo-methylations within island, shores and shelfs were remarkably similar between newly infected cells and established KSHV-associated malignancies despite a major over-all difference in scales of genome wide hypo-methylation, suggesting a progressive CpG hypo-methylation after KSHV infection. In an attempt to understand the mechanism of hypo-methylation induced by KSHV we have found that KSHV modulates the expression levels of the Ten-eleven translocation (TET) methylcytosine dioxygenases, a family of proteins involved in CpG de-methylation.