Chromatin association sites of KSHV and RRV PAN RNA

During lytic replication of Kaposi’s sarcoma-associated herpesvirus (KSHV), a nuclear viral long noncoding RNA known as PAN RNA becomes the most abundant polyadenylated transcript in the cell. Knockout or knockdown of KSHV PAN RNA results in loss of late lytic viral gene expression and, consequently, reduction of progeny virion release from the cell. We studied KSHV and RRV PAN RNA homologs using capture hybridization analysis of RNA targets (CHART) and observed their reproducible associations with host chromatin, but the loci differ between PAN RNA homologs. Examination of the binding sites of viral PAN RNA in KSHV-infected BCBL-1 cells and RRV-infected BJAB-RRV cells. Latent samples, as well as three timepoints of lytic viral induction were analyzed for each cell type (BCBL-1: 16 hr, 24 hr and 48 hr; BJAB-RRV: 18 hr, 24 hr, 36 hr).

在卡波西肉瘤相关疱疹病毒（Kaposi’s sarcoma-associated herpesvirus, KSHV）的裂解复制过程中，一种被命名为PAN RNA的病毒核内长链非编码RNA（long noncoding RNA）会成为细胞内丰度最高的多聚腺苷酸化转录本。敲除或敲低KSHV的PAN RNA会导致病毒晚期裂解基因表达丧失，并最终减少子代病毒粒子从细胞中的释放。本研究通过RNA靶标捕获杂交分析（capture hybridization analysis of RNA targets, CHART）对KSHV与RRV的PAN RNA同源物进行了研究，观察到二者均可重复地与宿主染色质结合，但二者的结合基因座存在差异。我们对KSHV感染的BCBL-1细胞以及RRV感染的BJAB-RRV细胞中的病毒PAN RNA结合位点进行了检测。针对每一种细胞系，我们均对其潜伏感染样本以及三个裂解病毒诱导时间点的样本进行了分析（BCBL-1细胞样本时间点：16小时、24小时与48小时；BJAB-RRV细胞样本时间点：18小时、24小时与36小时）。