Methylation dependent interactions of viral transcription factor Zta with DNA
Epstein Barr Virus, a human herpes virus associated with infectious mononucleosis, Burkitt’s lymphoma, Nasopharyngeal Carcinoma and Hodgkin’s disease, can infect B cells and establish latency. Zta, a member of the bZIP transcription factor family, is a viral transcription and replication factor required for activation of lytic cycle.\ud \ud Zta is able to bind DNA, through specific Zta Response Elements (ZREs). Interestingly, Zta binds in a methylation dependent manner to specific CpGcontaining ZREs, known as Class III ZREs. RpZRE3 is one of the first examples of such a site, and can be found in the promoter of a key viral lytic gene, BRLF1. Through computational analysis and in vitro binding assays, it was found that the core 7mer sequence of RpZRE3 is sufficient for complex formation in vitro, and that the core sequence can be found in a variety of human gene promoter regions. \ud \ud As more methylation dependent ZREs emerged, a method to predict CpGcontaining ZREs was devised using position frequency matrices, coupled with in vitro binding verification, leading to the discovery of 12 novel CpG containing methylation dependent ZREs. The regulatory regions of both the EBV genome (type 1) and the human genome were mapped for a list of experimentally verified ZRE core sequences (both methylation dependent and independent). This analysis allowed identification of novel viral and host genes, potentially under the control of Zta activation, which were further analysed using existing transcriptome and methylome data. \ud \ud An investigation into potential host factors using the same methylation dependent mechanism was started, and an unknown protein was seen to bind in a methylation dependent manner to RpZRE3 in the absence of Zta in vitro.