PA-seq for Global Identification of RNA Polyadenylation Sites of Kaposi's Sarcoma-Associated Herpesvirus Transcripts.
PA-seq for Global Identification of RNA Polyadenylation Sites of Kaposi's Sarcoma-Associated Herpesvirus Transcripts.
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PA-seq 用于卡波西肉瘤相关疱疹病毒转录本 RNA 多腺苷酸化位点的全局鉴定。
DOI：
10.1002/cpmc.1
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发表时间：
2016-05-06
影响因子：
--
通讯作者：
Zhu J
中科院分区：
文献类型：
--
作者：
Ni T;Majerciak V;Zheng ZM;Zhu J
卡波西肉瘤相关疱疹病毒（KSHV）是一种与免疫功能低下患者中几种恶性肿瘤的发生有关的人类肿瘤病毒。像其他疱疹病毒一样，KSHV有一个大的DNA基因组，编码100多种不同的基因产物。尽管被细胞机器转录和加工，但病毒基因组中KSHV基因的结构和组织与在人类基因组的细胞基因中观察到的不同。KSHV表达的一个典型特征是产生多顺反子转录物，这些转录物起始于不同的启动子，但共享相同的聚腺苷酸化位点（pA位点）。这代表了确定单个病毒转录物的3'端的挑战。这些信息对于生成用于遗传研究的病毒转录图谱至关重要。在这里，我们提出了PA-seq，一个高通量的方法，用于全基因组分析的PA网站的KSHV转录本在B淋巴细胞与潜伏性或溶解性KSHV感染。除了鉴定所有病毒pA位点外，PA-seq还提供了关于与每个pA位点相关的病毒转录物水平的定量信息，从而能够确定病毒基因在感染的各个阶段的相对表达水平。由于PA-seq的不加选择的性质，宿主转录物的pA位点也同时定位在测试样品中。因此，该技术可以同时估计KSHV感染后宿主基因的表达变化和RNA多聚腺苷酸化。
Kaposi sarcoma-associated herpesvirus (KSHV) is a human oncovirus linked to the development of several malignancies in immunocompromised patients. Like other herpesviruses, KSHV has a large DNA genome encoding more than 100 distinct gene products. Despite being transcribed and processed by cellular machinery, the structure and organization of KSHV genes in the virus genome differs from that observed in cellular genes from the human genome. A typical feature of KSHV expression is the production of polycistronic transcripts initiated from different promoters but sharing the same polyadenylation site (pA site). This represents a challenge in determination of the 3' end of individual viral transcripts. Such information is critical for generation of a virus transcriptional map for genetic studies. Here we present PA-seq, a high-throughput method for genome-wide analysis of pA sites of KSHV transcripts in B lymphocyte with latent or lytic KSHV infection. Besides identification of all viral pA sites, PA-seq also provides quantitative information about the levels of viral transcripts associated with each pA site enabling to determine the relative expression levels of viral genes at various stages of infection. Due to the indiscriminate nature of PA-seq, the pA sites of host transcripts are also concurrently mapped in the testing samples. Therefore, this technology can simultaneously estimate the expression changes of host genes and RNA polyadenylation upon KSHV infection.