Researchers created the most comprehensive study of how the viral genome interacts with its human host during a latent infection. Italo Tempera who took part to the study, explains the research's topics.

Viruses are tiny and powerful pathogens that evolved to interfere with the host cell’s homeostasis and establish favorable conditions for the viral infection. To reach their goal viruses have adopted different strategies that aim to hijack the host gene expression and exploit it to support viral gene translation.

Epigenetic modifications play a crucial role in gene expression regulation and a number of recent discoveries underscore how changes in the epigenome are instrumental in rapidly reprogramming gene expression in response to external stimuli. Thus epigenetic modifications and changes in epigenome represent another target of viral infection. However, how viruses exploit the host epigenetic machinery and the impact of viral infection on the host genome depend largely on the biology of the viruses.

In our study we focused our attention on one of the most extensively characterized tumor viruses: Epstein-Barr virus (EBV). EBV is a human gammaherpesvirus that is present in 95% of the population worldwide. EBV is the etiological agent of infectious mononucleosis and is also associated with B-cell and epithelial malignancies, including endemic Burkitt’s lymphoma, nasopharyngeal carcinoma, ~50% of Hodgkin’s disease, and lymphoproliferative disorders of immunosuppressed individuals. EBV is estimated to be responsible for ~1% of all human cancers.

Using genome-wide analysis of histone modifications coupled with methods to indentify high-order chromatin conformations we studied at a genomic scale how EBV exploits/employs the host epigenetic machinery to control its own multiplication and the immune evasion. To generate an atlas of functional elements for EBV genome we analyzed more than 300 large-scale functional genomic data sets for EBV positive cells.

The chromatin profile of EBV showed that the viral genome is partitioned into well organized regulatory regions which chromatin composition changes with respect to the stage of B-cell differentiation and the type of tumor from which the cells are obtained. In particular in undifferentiated B-cells and in lymphoblastoid cell lines the viral genome is associated with a more relaxed chromatin structure that is more accessible to the transcription machinery. Conversely in B-memory cells and in healthy individuals EBV genome tends to be associated with a more compact chromatin structure that is a less accessible to the translational machinery. These findings show that epigenetic modifications are important regulative component of the immune evasion and carcinogenic risk of EBV.

We also analyzed binding profiles for over 60 human transcription factors across EBV genome. This analysis provided a systemic means to reveal specific characteristics of EBV genome that relate to the ways in which the virus interacts with its own host. We identified at least 26 human transcription factors, including factors involved in B cell development and viral response, such as Pax5, Irf3, EBF1 and NFKB, that have significant binding sites across the viral genome. These data suggest that EBV hijack the host control pathways to regulate the expression of viral oncogenes and contribute to tumorigenesis.

Finally we further explore the EBV chromosome architecture and its impact on viral translation. We found that host factors involved in the chromatin organization and long-distance DNA looping formation such as CTCF, SMC1, SMC3 and Rad21 bound several loci across the viral genome. Moreover, we found that by interacting with these proteins EBV is able to adopt alternative chromosome conformations that bring regulatory regions in close proximity to viral promoters, contributing to finely tuning viral gene expressions.

Taken together our data provide a comprehensive atlas of functional elements of EBV. The combined analysis of histone modification patterns, combinatorial transcription factors, and long-range DNA looping, gives a new insight into host-virus interactions and how EBV exploits the host epigenetic machinery to control viral gene expression. As epigenetic drugs are used in cancer therapy, underlying the role of histone modifications on regulating EBV infection provides a new target for therapeutic treatment of EBV positive tumors. Also, as in other examples of cell biology, viral model systems are instrumental in expanding our knowledge about similar mechanisms that occur in mammalian cells.