Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing.
Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing.
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DOI：
10.1371/journal.ppat.1005166
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发表时间：
2015-09
期刊：
影响因子：
6.7
通讯作者：
Carmichael GG
中科院分区：
文献类型：
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作者：
Garren SB;Kondaveeti Y;Duff MO;Carmichael GG
小鼠多瘤病毒（MPyV）溶解性感染小鼠细胞，在培养中转化大鼠细胞，并在啮齿动物中高度致癌。我们利用深度测序技术对感染后不同时间小鼠NIH3T6细胞的MPyV感染进行了跟踪，并分析了病毒和细胞转录组。测序读数与病毒基因组的比对说明了早到晚转换的转录谱，即早链rna和晚链rna在所有时间点都被转录。从这些研究中出现了许多关于病毒基因表达的新见解，包括证明在感染后期对病毒转录物进行广泛的RNA编辑。在感染后期，359个宿主基因被观察到显著上调，857个被下调。基因本体论分析表明，涉及翻译、代谢、RNA加工、DNA甲基化和蛋白质转换的转录本上调，而涉及细胞外粘附、细胞骨架、锌指结合、SH3结构域和GTPase激活的转录本下调。一些长链非编码rna的水平也发生了改变。参与拼接斑点的长链非编码RNA MALAT1在许多晚期癌症中被用作标记物，明显下调，而其他一些丰富的非编码RNA则强烈上调。我们根据目前已知的MPyV生命周期及其对宿主细胞生长和代谢的影响来讨论这些结果。小鼠多瘤病毒（MPyV）是一种小的5.3kb环状双链DNA病毒，能够在免疫功能低下的小鼠的多种组织中引起肿瘤。60多年来，它一直是一个研究课题，对肿瘤发生、细胞周期信号传导和转化等一系列过程有了深入的了解。本研究利用Illumina测序技术观察病毒和宿主细胞总RNA的变化，并应用新方法更直接地确认宿主ADAR酶对病毒RNA进行a -to- i编辑的程度，从而提供了MPyV感染的全局视图。这允许同时观察宿主和病毒的转录变化，这些变化是由于早期基因表达和病毒从早期基因到晚期基因的转换而发生的，这种转换与DNA复制的开始一致。
Mouse polyomavirus (MPyV) lytically infects mouse cells, transforms rat cells in culture, and is highly oncogenic in rodents. We have used deep sequencing to follow MPyV infection of mouse NIH3T6 cells at various times after infection and analyzed both the viral and cellular transcriptomes. Alignment of sequencing reads to the viral genome illustrated the transcriptional profile of the early-to-late switch with both early-strand and late-strand RNAs being transcribed at all time points. A number of novel insights into viral gene expression emerged from these studies, including the demonstration of widespread RNA editing of viral transcripts at late times in infection. By late times in infection, 359 host genes were seen to be significantly upregulated and 857 were downregulated. Gene ontology analysis indicated transcripts involved in translation, metabolism, RNA processing, DNA methylation, and protein turnover were upregulated while transcripts involved in extracellular adhesion, cytoskeleton, zinc finger binding, SH3 domain, and GTPase activation were downregulated. The levels of a number of long noncoding RNAs were also altered. The long noncoding RNA MALAT1, which is involved in splicing speckles and used as a marker in many late-stage cancers, was noticeably downregulated, while several other abundant noncoding RNAs were strongly upregulated. We discuss these results in light of what is currently known about the MPyV life cycle and its effects on host cell growth and metabolism. Mouse polyomavirus (MPyV) is a small 5.3kb circular double-stranded DNA virus capable of causing tumors in a variety of tissues in immunocompromised mice. It has been a subject of study for over 60 years, yielding insights into a number of processes including tumorigenesis, cell cycle signaling, and transformation. This study serves to provide a global view of the MPyV infection by utilizing Illumina sequencing to observe changes in total RNA from both the virus and the host cell as well as applying new methods to more directly confirm the extent of A-to-I editing of viral RNA by host ADAR enzymes. This allows for a simultaneous observation of both host and viral transcriptional changes that occur as a result of early gene expression and the viral switch from early to late genes that occurs coincident with the initiation of DNA replication.