Epigenetic Regulation of KSHV Latency

PROJECT SUMMARY Kaposi’s sarcoma-associated herpesvirus (KSHV) causes several AIDS-defining malignancies including Kaposi’s sarcoma (KS), the most common oral cancer affecting people with HIV. Persistence of KSHV cancers is rooted in the ability of the virus to establish life-long latency, a dormancy-like phase where no virions are produced, and gene transcription is restricted to the latency genes to drive tumor cell survival and proliferation. In latency, KSHV represses lytic genes that are typically used for viral replication and propagation to evade immune surveillance. Majority of primary tumor cells are latently infected with only <5% of cells supporting lytic replication which is necessary for dissemination. Thus, the balance of latency and lytic transcriptional programs is crucial to KSHV malignancies. Our long-term goal is to understand mechanisms underlying the control of the latency and lytic transcriptional programs. We and others have shown that the latency-lytic balance is coordinated by the organization of the viral genome. However, it remains unknown how these higher order structures are initially formed or how they are maintained after latency is established. Using a CRISPR/CasRx screen tiling the KSHV genome, we recently discovered that a novel long non-coding RNA (lncRNA) from the origin of lytic replication (OriLytL) is critical for viral latency (OriLytL-lat RNA). This was surprising because the OriLytL is only known to function during lytic replication and not during latency. Based on our preliminary data and strategic positioning of this latent lncRNA at the origin of lytic replication, the central hypothesis of this proposal is the OriLytL-lat RNA mediates the latent-lytic balance by driving chromatin remodeling and genome localization. Specifically, we will study how this lncRNA organizes the viral chromatin structure before and after establishing latency. In addition, we will investigate how this directs the spatial localization of the latent chromatin which has now emerged to be a major factor of gene regulation. Together, these Aims will define mechanisms of latency establishment and maintenance which are key to KSHV malignancies.