Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity [ATAC-seq]. Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity [ATAC-seq]

Human cytomegalovirus (HCMV) infects up to 80% of the world’s population and is linked to serious morbidity in immunocompromised individuals and newborns. Here, using multiple genome-scale assays and computational approaches, we show that HCMV infection leads to widespread changes in chromatin accessibility and chromatin looping, with hundreds of thousands of human genomic regions affected 48 hours after infection. Integrative analyses reveal that HCMV infection perturbs the Hippo signaling pathway by drastically diminishing TEA domain transcription factor 1 (TEAD1) activity. Chromatin immunoprecipitation experiments confirm extensive concordant loss of TEAD1 binding and H3K27ac active histone marks upon infection. TEAD transcription factors are direct effectors of the Hippo signaling pathway, and our data support a position for TEAD1 at the top of a hierarchy involving key developmental pathways with differential expression subsequent to HMCV infection. Known gene targets of TEAD1, including Cellular Communication Network Factor 1 (CCN1) and Thrombospondin 1 (THBS1), are significantly downregulated with HCMV infection, reflecting diminished TEAD1-mediated activity. HCMV infection reduces TEAD1 binding through four distinct mechanisms: closing of TEAD1-bound chromatin, reduction of Yes1 associated transcriptional regulator (YAP1) and phosphorylated YAP (pYAP1) levels, reduction of TEAD1 transcript and protein levels, and alteration of TEAD1 exon-6 usage. Collectively, these comprehensive genome-scale analyses reveal novel mechanisms induced by HCMV infection. Overall design: We performed ATAC-seq in two human cell lines in two conditions. The cell lines are foreskin fibroblasts (HS68) and retinal epithelial (ARPE-19). The two conditions are: 1) uninfected; and 2) 48 hours post infection of human cytomegalovirus (HCMV) with the TB40/E clinical isolate. Experiments were performed in two replicates for each cell type and condition combination.

人巨细胞病毒（Human cytomegalovirus, HCMV）可感染全球多达80%的人口，与免疫功能低下人群及新生儿的严重发病密切相关。本研究通过多组基因组规模实验与计算分析方法，证实HCMV感染可引发染色质开放状态与染色质环结构的广泛改变，感染后48小时内即有数十万个人类基因组区域受到影响。整合分析显示，HCMV感染通过显著降低TEA结构域转录因子1（TEA domain transcription factor 1, TEAD1）的活性，干扰Hippo信号通路。染色质免疫共沉淀实验证实，感染后TEAD1结合位点与H3K27ac活性组蛋白修饰均出现广泛且一致的丢失。TEAD转录因子是Hippo信号通路的直接效应分子，本研究数据表明，TEAD1处于关键发育通路调控层级的顶端，这些通路的基因表达在HCMV感染后出现差异变化。已知的TEAD1靶基因包括细胞通讯网络因子1（Cellular Communication Network Factor 1, CCN1）与血小板反应蛋白1（Thrombospondin 1, THBS1），在HCMV感染后显著下调，这反映了TEAD1介导的活性被削弱。HCMV感染通过四种不同机制降低TEAD1的结合能力：一是关闭TEAD1结合的染色质区域，二是降低Yes1相关转录调控因子（Yes1 associated transcriptional regulator, YAP1）及其磷酸化形式pYAP1的水平，三是减少TEAD1的转录本与蛋白表达量，四是改变TEAD1的第6号外显子剪接使用模式。综上，这些全面的基因组规模分析揭示了HCMV感染诱导的全新分子机制。实验设计概述：本研究在两种人类细胞系的两种培养条件下开展ATAC-seq实验，所用细胞系为包皮成纤维细胞（HS68）与视网膜上皮细胞（ARPE-19）；两种培养条件分别为：1）未感染组；2）感染TB40/E临床分离株HCMV后48小时组。每种细胞系与条件的组合均设置两次生物学重复。