The establishment of latency is an essential step for the life-long
persistent infection and pathogenesis of Kaposi's sarcoma-associated herpesvirus (KSHV). While the KSHV genome is
chromatin-free in the virions, the
viral DNA in latently infected cells has a
chromatin structure with activating and repressive histone modifications that promote latent gene expression but suppress lytic gene expression. Here, we report a comprehensive epigenetic study of the recruitment of
chromatin regulatory factors onto the KSHV genome during the pre-latency phase of KSHV
infection. This demonstrates that the KSHV genome undergoes a biphasic chromatinization following de novo
infection. Initially, a transcriptionally active
chromatin (
euchromatin), characterized by high levels of the
H3K4me3 and acetylated H3K27 (H3K27ac) activating histone marks, was deposited on the viral episome and accompanied by the transient induction of a limited number of lytic genes. Interestingly, temporary expression of the RTA
protein facilitated the increase of
H3K4me3 and H3K27ac occupancy on the KSHV episome during de novo
infection. Between 24-72 hours post-
infection, as the levels of these activating histone marks declined on the KSHV genome, the levels of the repressive H3K27me3 and H2AK119ub histone marks increased concomitantly with the decline of lytic gene expression. Importantly, this transition to
heterochromatin was dependent on both
Polycomb Repressive Complex 1 and 2. In contrast, upon
infection of human gingiva-derived epithelial cells, the KSHV genome underwent a transcription-active euchromatinization, resulting in efficient lytic gene expression. Our data demonstrate that the KSHV genome undergoes a temporally-ordered biphasic
euchromatin-to-
heterochromatin transition in endothelial cells, leading to
latent infection, whereas KSHV preferentially adopts a transcriptionally active
euchromatin in oral epithelial cells, resulting in lytic gene expression. Our results suggest that the differential epigenetic modification of the KSHV genome in distinct cell types is a potential determining factor for
latent infection versus lytic replication of KSHV.