Human Papillomavirus Genomes Associate with Active Host Chromatin during Viral Genome Maintenance [ATAC-seq]

Human papillomaviruses (HPVs) maintain their genomes as minichromosomes in the nuclei of infected keratinocytes. This study investigates the association of HPV31 genomes with host chromatin using both HiC and 4C-seq chromosome conformation capture techniques. We show that HPV31 genomes preferentially associate with transcriptionally active A compartments of host chromatin, regions of open chromatin defined by ATAC-seq, and super-enhancers defined by Brd4 and H3K27ac ChIP-seq. The viral genome association sites were also highly correlated with genomic loci previously identified as common HPV integration sites in cervical cancers. Recent studies have shown that transcriptionally active sites are prone to dsDNA breaks, and we find a strong correlation among dsBREAK datasets with transcriptionally active and open regions of host chromatin and the HPV31 genome association sites defined in our study. These findings suggest that HPV genomes associate with cellular transcriptional epicenters to maintain active viral gene expression during persistent infection, but also indicate that the susceptibility of these regions to dsDNA breaks could explain their propensity for viral DNA integration in HPV-associated cancers. Overall design: ATAC-seq analysis of growing and calcium-induced differentiated CIN612-9E cervical keratinocytes that were untreated or treated for 48 hours with 0.5 µM keratinocyte differentiation inducer (KDi) for the differentiated condition only.

人乳头瘤病毒（Human papillomaviruses, HPVs）会以微染色体的形式在受感染角质形成细胞的细胞核内维持自身基因组。本研究采用HiC及4C-seq两种染色体构象捕获技术，探究HPV31基因组与宿主染色质的相互结合关联。本研究发现，HPV31基因组优先与宿主染色质的转录活跃A区室、经ATAC-seq鉴定的开放染色质区域，以及经Brd4和H3K27ac ChIP-seq鉴定的超级增强子发生结合。病毒基因组的结合位点还与此前在宫颈癌组织中鉴定出的常见HPV整合位点基因组区域高度相关。已有研究证实，转录活跃的区域易于发生双链DNA断裂（double-strand DNA breaks, dsDNA breaks）；本研究发现，dsBREAK数据集与宿主染色质的转录活跃区域、开放染色质区域，以及本研究鉴定的HPV31基因组结合位点之间存在显著相关性。上述研究结果表明，HPV基因组可通过结合细胞转录核心区域，在持续感染过程中维持病毒基因的活跃表达；同时也提示，这些区域对双链DNA断裂的易感性，或可解释其在HPV相关癌症中易于发生病毒DNA整合的倾向。实验整体设计：对增殖状态及经钙诱导分化的CIN612-9E宫颈角质形成细胞开展ATAC-seq分析；其中增殖组细胞未作任何处理，分化组细胞则经0.5 μM角质形成细胞分化诱导剂（keratinocyte differentiation inducer, KDi）处理48小时。