The chromatin loop release factor WAPL regulates EBV latency status by restricting LMP production [HiChIP]

Epstein-Barr virus (EBV) is a ubiquitous human pathogen that is etiologically linked to several cancers and has been connected to multiple sclerosis. EBV persists in its human hosts through a biphasic replication cycle that depends on three latency stages. Understanding the host mechanisms that contribute to the tight regulation of viral gene expression in the discrete states of latency III, latency II, and latency I is important for developing therapeutic approaches for treating EBV positive cancers. Regulation of the chromatin structure of the EBV genome by cohesin and CTCF plays a role in this latency type switching. However, the function of the cohesin release factor WAPL had not previously been understood. In this study, we employ RNA-seq combined with immunofluorescence analysis to determine that the cohesin release factor WAPL plays a role specifically in inhibiting the expression of the oncogenic latent membrane proteins LMP-1 and LMP-2A. Through a combination of Hi-ChIP and ChIP-qPCR, we uncover that WAPL loss alters the looping interactions within the EBV genome and alters the histone modifications present at the LMP promoter. We propose that EBV coopts WAPL to maintain a latency I state and, without WAPL, leaky expression of the LMP proteins occurs. Overall design: Hi-ChIP was performed as previously descibed. WAPL was knocked out in MUTU I cells via CRISPR-Cas9 or an sgControl guide RNA was used. ChIP for H3K27Ac was performed.