Next-generation sequencing of small RNAs from HIV-infected cells identifies phased microrna expression patterns and candidate novel microRNAs differentially expressed upon infection.
Next-generation sequencing of small RNAs from HIV-infected cells identifies phased microrna expression patterns and candidate novel microRNAs differentially expressed upon infection.
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DOI：
10.1128/mbio.00549-12
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发表时间：
2013-02-05
期刊：
影响因子：
6.4
通讯作者：
Katze MG
中科院分区：
文献类型：
--
作者：
Chang ST;Thomas MJ;Sova P;Green RR;Palermo RE;Katze MG
HIV感染的CD 4 + T细胞诱导一系列宿主mRNA转录变化以及可能协调mRNA变化的microRNA。为了调查这些动态变化，我们应用下一代测序，分析感染后5、12和24小时艾滋病毒感染细胞的小RNA部分（RNA-Seq）。这些时间点提供了在病毒复制之前和期间发生的转录组学变化的视图。在由此产生的小RNA-Seq数据集中，我们检测到microRNA表达的阶段性模式。发现在感染后5和12 h，大量不同的microRNA组被抑制，并且这两组变化在感染后反弹。在感染后24 h观察到一组较大的microRNA变化。当与mRNA表达数据整合时，小RNA-Seq数据表明microRNA在HIV感染期间的转录调控，T细胞活化和细胞周期中的作用。作为下一代测序的一个独特优势，我们还检测到了在感染过程中差异表达的候选新宿主microRNA，其中包括一种在感染后24小时下调的可能允许HIV完全复制的microRNA。总的来说，我们的数据提供了一个独特的全面的观点，在细胞感染过程中由HIV诱导的宿主microRNA的变化。新的测序技术允许对病毒感染细胞中发生的变化进行前所未有的观察，包括对不同类型RNA的全面和基本上无偏见的测量。在这项研究中，我们使用下一代测序来分析HIV感染细胞中细胞microRNA的动态变化。测序提供的灵敏度使我们能够在病毒复制开始之前检测感染早期microRNA表达的变化。在这些microRNA中，明显存在阶段性表达模式，许多最初被抑制的microRNA后来在感染高峰时过度表达，提供了独特的感染特征。通过整合额外的mRNA数据与microRNA数据，我们确定了microRNA在感染过程中的转录调控作用，特别是参与已知HIV辅因子表达的microRNA网络。最后，作为测序的一个明显好处，我们鉴定了候选的未注释的microRNA，包括一个下调可能允许HIV-1复制完全进行的microRNA。
HIV infection of CD4+ T cells induces a range of host transcriptional changes in mRNAs as well as microRNAs that may coordinate changes in mRNAs. To survey these dynamic changes, we applied next-generation sequencing, analyzing the small RNA fraction of HIV-infected cells at 5, 12, and 24 h postinfection (RNA-Seq). These time points afforded a view of the transcriptomic changes occurring both before and during viral replication. In the resulting small RNA-Seq data set, we detected a phased pattern of microRNA expression. Largely distinct sets of microRNAs were found to be suppressed at 5 and 12 h postinfection, and both sets of changes rebounded later in infection. A larger set of microRNA changes was observed at 24 h postinfection. When integrated with mRNA expression data, the small RNA-Seq data indicated a role for microRNAs in transcriptional regulation, T cell activation, and cell cycle during HIV infection. As a unique benefit of next-generation sequencing, we also detected candidate novel host microRNAs differentially expressed during infection, including one whose downregulation at 24 h postinfection may allow full replication of HIV to proceed. Collectively, our data provide a uniquely comprehensive view of the changes in host microRNAs induced by HIV during cellular infection. New sequencing technologies allow unprecedented views into changes occurring in virus-infected cells, including comprehensive and largely unbiased measurements of different types of RNA. In this study, we used next-generation sequencing to profile dynamic changes in cellular microRNAs occurring in HIV-infected cells. The sensitivity afforded by sequencing allowed us to detect changes in microRNA expression early in infection, before the onset of viral replication. A phased pattern of expression was evident among these microRNAs, and many that were initially suppressed were later overexpressed at the height of infection, providing unique signatures of infection. By integrating additional mRNA data with the microRNA data, we identified a role for microRNAs in transcriptional regulation during infection and specifically a network of microRNAs involved in the expression of a known HIV cofactor. Finally, as a distinct benefit of sequencing, we identified candidate nonannotated microRNAs, including one whose downregulation may allow HIV-1 replication to proceed fully.