Integrated analyses reveal CHD4 mediating establishment and maintainence of latent KSHV chromatin

The overall goal of these studies was to define the long-range chromatin interactions occurring within the KSHV genome as well as between the KSHV and human host cell genomes both during latency and viral reactivation. These were defined in an unbiased manner using Hi-C analysis, which is chromosome conformation capture (3C) combined with next-generation sequencing (NGS). A modified protocol, referred to as Capture Hi-C, was utilized to selectively enrich interactions involving KSHV by performing target enrichment with a custom-designed KSHV genomic capture probe library. Experiments were performed in three different KSHV naturally infected human primary effusion lymphoma (PEL) cell lines (TREx-F3H3-K-Rta BCBL-1, BC1 and BC3) and wild type or ORF57-Stop recombinant KSHV infected iSLK cells.