Viral disruption of host transcriptome integrity

大多数病毒感染引起宿主基因表达的重大变化，作为为病毒复制创造最佳环境的更广泛策略的一部分。通过抑制宿主蛋白合成，病毒重新利用宿主细胞的生物合成资源，最大限度地积累病毒蛋白或核酸，从而最终提高新的感染性后代的产量。1型单纯疱疹病毒（HSV-1）提供了这种重要的“宿主关闭”现象的一个主要例子。HSV-1感染伴随着RNA聚合酶II转录的失调，伴随着mRNA稳定性、剪接、3 '端形成和转录终止的改变，导致宿主mRNA生物发生的广泛破坏。尽管多项研究表明，必需的病毒调节蛋白ICP27参与了HSV-1的关闭，但其确切机制及其相对作用仍有待阐明。最近，我们证明了HSV-1感染引起宿主核因子亚细胞定位的广泛变化，这些亚细胞定位是安装、去除和识别内部RNA修饰所必需的，包括腺苷（m6A） n6位置的甲基化。这导致宿主和病毒rna上存在的内部碱基修饰的全局减少。重要的是，我们确定了必需的病毒调节蛋白ICP27对于这种惊人的效果既是必要的，也是充分的。m6A等内部RNA修饰影响mRNA和lncRNA生物发生的许多方面，包括对硬连接剪接和切割/聚腺苷化信号的识别，m6A还调节成熟mRNA的输出、稳定性和翻译。我们观察到，病毒基因表达在感染周期开始时对m6A的缺失很敏感，但在后期受到的影响较小，这与RNA修饰频率降低相一致。结合这些观察结果，我们提出，ICP27广泛破坏宿主基因表达的能力，至少在一定程度上是通过其重新定义宿主转录组的表观遗传景观的能力介导的。为了更好地理解这一点，我们将更全面地表征ICP27表达对负责RNA化学修饰和3 '端加工和转录终止的宿主机制的影响。最近的研究揭示了m6A的位置与附近多聚腺苷化和信号的使用之间的机制联系，我们假设ICP27利用这一点在HSV-1感染细胞中引起广泛的转录终止中断（DoTT），优先影响宿主转录组。为了理解为什么HSV-1 mrna的3 '端形成对ICP27介导的DoTT不敏感，我们将分析m6A在病毒转录组中的安装情况，以确定m6A对病毒转录单元内切割和聚腺苷化位点使用的影响。

Most viral infections invoke major changes in host gene expression as part of a broader strategy to create an optimal environment for viral replication. By suppressing host protein synthesis, viruses repurpose the biosynthetic resources of the host cell to maximize the accumulation of viral proteins or nucleic acids and thus ultimately boost the yield of new infectious progeny. Herpes simplex virus type 1 (HSV-1) provides a prime example of this important ‘host shutoff’ phenomenon. HSV-1 infection is accompanied by widescale disruption of host mRNA biogenesis through dysregulation of transcription by RNA polymerase II coupled with changes in mRNA stability, splicing, 3’-end formation, and transcription termination. Although multiple studies have implicated the essential viral regulatory protein ICP27 in aspects of shutoff by HSV-1, the exact mechanisms and their relative contributions remain to be elucidated. Recently, we demonstrated that HSV-1 infection induces widespread changes in the subcellular localization of host nuclear factors required for the installation, removal and recognition of internal RNA modifications including methylation at the N6-position of adenosine (m6A). This results in global reductions in the internal base modifications present on both host and viral RNAs. Importantly, we identified the essential viral regulatory protein ICP27 as both necessary and sufficient for this striking effect. Internal RNA modifications such as m6A influence many aspects of mRNA and lncRNA biogenesis including recognition of hardwired splicing and cleavage/polyadenylation signals, and m6A also regulates the export, stability and translation of mature mRNAs. We observed that viral gene expression is sensitive to loss of m6A at the beginning of the infection cycle but is less impacted at later times, coincident with reduced RNA modification frequency. Drawing these observations together we propose that the poorly understood ability of ICP27 to broadly disrupt host gene expression is mediated, at least in part, by its ability to redefine the epigenetic landscape of the host transcriptome. To understand this better, we will more fully characterize the impact of ICP27 expression on the host machinery responsible for RNA chemical modification and for 3’-end processing and transcription termination. Recent studies reveal a mechanistic linkage between the sites of m6A placement and use of nearby polyadenylation and signals and we hypothesize that this is exploited by ICP27 to bring about a widescale disruption of transcription termination (DoTT) that preferentially impacts the host transcriptome in HSV-1 infected cells. To understand why 3’-end formation of HSV-1 mRNAs is largely insensitive to ICP27- mediated DoTT, we will profile m6A installation across the viral transcriptome to determine the impact of m6A on cleavage and polyadenylation site usage within viral transcription units.