Department of Viroscience, Erasmus MC, Rotterdam, Netherlands.
Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan.
mBio. 2020 Oct 6;11(5):e01568-20. doi: 10.1128/mBio.01568-20.
Varicella-zoster virus (VZV), a double-stranded DNA virus, causes varicella, establishes lifelong latency in ganglionic neurons, and reactivates later in life to cause herpes zoster, commonly associated with chronic pain. The VZV genome is densely packed and produces multitudes of overlapping transcripts deriving from both strands. While 71 distinct open reading frames (ORFs) have thus far been experimentally defined, the full coding potential of VZV remains unknown. Here, we integrated multiple short-read RNA sequencing approaches with long-read direct RNA sequencing on RNA isolated from VZV-infected cells to provide a comprehensive reannotation of the lytic VZV transcriptome architecture. Through precise mapping of transcription start sites, splice junctions, and polyadenylation sites, we identified 136 distinct polyadenylated VZV RNAs that encode canonical ORFs, noncanonical ORFs, and ORF fusions, as well as putative noncoding RNAs (ncRNAs). Furthermore, we determined the kinetic class of all VZV transcripts and observed, unexpectedly, that transcripts encoding the ORF62 protein, previously designated , were expressed with kinetics. Our work showcases the complexity of the VZV transcriptome and provides a comprehensive resource that will facilitate future functional studies of coding RNAs, ncRNAs, and the biological mechanisms underlying the regulation of viral transcription and translation during lytic VZV infection. Transcription from herpesviral genomes, executed by the host RNA polymerase II and regulated by viral proteins, results in coordinated viral gene expression to efficiently produce infectious progeny. However, the complete coding potential and regulation of viral gene expression remain ill-defined for the human alphaherpesvirus varicella-zoster virus (VZV), causative agent of both varicella and herpes zoster. Here, we present a comprehensive overview of the VZV transcriptome and the kinetic class of all identified viral transcripts, using two virus strains and two biologically relevant cell types. Additionally, our data provide an overview of how VZV diversifies its transcription from one of the smallest herpesviral genomes. Unexpectedly, the transcript encoding the major viral transactivator protein (pORF62) was expressed with kinetics, whereas orthologous transcripts in other alphaherpesviruses are typically expressed during the immediate early phase. Therefore, our work both establishes the architecture of the VZV transcriptome and provides insight into regulation of alphaherpesvirus gene expression.
水痘带状疱疹病毒（VZV）是一种双链 DNA 病毒，可引起水痘，在神经节神经元中建立终身潜伏，并在以后的生活中重新激活，导致带状疱疹，通常与慢性疼痛有关。VZV 基因组紧密包装，并产生大量来自两条链的重叠转录本。虽然迄今为止已经通过实验定义了 71 个不同的开放阅读框（ORF），但 VZV 的全部编码潜力仍未知。在这里，我们将多种短读 RNA 测序方法与从 VZV 感染细胞中分离的 RNA 的长读直接 RNA 测序相结合，提供了对裂解 VZV 转录组结构的全面重新注释。通过精确映射转录起始位点、剪接接头和多聚腺苷酸化位点，我们鉴定了 136 种不同的多聚腺苷酸化 VZV RNA，这些 RNA 编码规范 ORF、非规范 ORF 和 ORF 融合，以及推定的非编码 RNA（ncRNA）。此外，我们确定了所有 VZV 转录物的动力学类别，并出人意料地观察到，先前指定为 的 ORF62 蛋白编码转录物以 动力学表达。我们的工作展示了 VZV 转录组的复杂性，并提供了一个全面的资源，将促进未来对编码 RNA、ncRNA 以及裂解 VZV 感染过程中病毒转录和翻译调节的生物学机制的功能研究。由宿主 RNA 聚合酶 II 执行并受病毒蛋白调节的疱疹病毒基因组转录导致协调的病毒基因表达，以有效地产生感染性后代。然而，人类α疱疹病毒水痘带状疱疹病毒（VZV）的完整编码潜力和病毒基因表达的调节仍未明确，VZV 是水痘和带状疱疹的病原体。在这里，我们使用两种病毒株和两种生物学上相关的细胞类型，对 VZV 转录组和所有鉴定的病毒转录物的动力学类别进行了全面概述。此外，我们的数据提供了一个概述，说明 VZV 如何从最小的疱疹病毒基因组之一多样化其转录。出乎意料的是，编码主要病毒反式激活蛋白（pORF62）的转录物以 动力学表达，而其他α疱疹病毒中的同源转录物通常在早期早期表达。因此，我们的工作既建立了 VZV 转录组的结构，又提供了对α疱疹病毒基因表达调控的深入了解。
