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.

本研究的总体目标为明确卡波西肉瘤相关疱疹病毒（KSHV）基因组内部，以及病毒潜伏感染与激活阶段中，KSHV与人类宿主细胞基因组之间存在的远程染色质相互作用。此类相互作用通过无偏倚实验策略，借助Hi-C分析得以解析——该技术将染色体构象捕获（chromosome conformation capture，3C）与下一代测序（next-generation sequencing，NGS）相结合。研究采用了一种名为捕获Hi-C（Capture Hi-C）的改良实验方案，通过定制化设计的KSHV基因组捕获探针文库开展靶标富集，从而选择性富集涉及KSHV的染色质相互作用。实验分别在3株天然感染KSHV的人类原发性渗出性淋巴瘤（PEL，primary effusion lymphoma）细胞系（TREx-F3H3-K-Rta BCBL-1、BC1及BC3），以及野生型或ORF57-Stop重组KSHV感染的iSLK细胞中完成。