MicroRNA levels are modulated in Aedes aegypti after exposure to Dengue-2.
MicroRNA levels are modulated in Aedes aegypti after exposure to Dengue-2.
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DOI：
10.1111/imb.12070
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发表时间：
2014-02
影响因子：
2.6
通讯作者：
Ebel GD
中科院分区：
文献类型：
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作者：
Campbell CL;Harrison T;Hess AM;Ebel GD
为了确定埃及伊蚊感染虫媒病毒期间微小RNA（miRNA）的参与情况，我们挖掘了登革热2型（DENV2）感染蚊子的深度测序文库。每个时间点（感染后2、4和9天（dpe））和处理组都有三个生物学重复，这使我们能够去除与样本间变异相关的异常值。利用专为处理重复深度测序数据而设计的edgeR（R生物信息学软件包），我们确定了miRNA水平（18 - 23个核苷酸）的对数倍数变化（logFC）。显著调节的miRNA数量从感染后2天和4天的5个或更少增加到感染后9天的23种独特的miRNA。通过将miRNA与转录组进行比对来预测假定的miRNA靶点，并将列表精简为包含使用Miranda、PITA和TargetScan算法找到的命中结果的交集。为了进一步减少假阳性，通过将假定靶点与近期登革热2型宿主反应转录组报告中报道的mRNA进行交叉核对来验证它们；确定了4076个靶点。其中，464个基因靶点在3′非翻译区（3′UTRs）具有预测的miRNA结合位点。特定情境下的靶点功能组包括参与运输、转录调控、线粒体功能、染色质修饰和信号转导过程的蛋白质，这些过程已知是病毒复制和传播所必需的。通过将预测靶点与转录组研究的靶点进行比较，将miRNA反应与其他媒介宿主反应研究联系起来。总之，这些数据与在登革热2型感染蚊子中基因表达发生深刻且持续变化的假设相一致。
To define microRNA (miRNA) involvement during arbovirus infection of Aedes aegypti, we mined deep sequencing libraries of Dengue type 2 (DENV2) -exposed mosquitoes. Three biological replicates for each timepoint (2, 4, and 9 days post-exposure (dpe)) and treatment group allowed us to remove outliers associated with sample-to-sample variability. Using edgeR (R Bioconductor), designed for use with replicate deep sequencing data, we determined the log fold-change (logFC) of miRNA levels (18–23 nts). The number of significantly modulated miRNAs increased from 5 or fewer at 2 and 4 dpe to 23 unique miRNAs by 9 dpe. Putative miRNA targets were predicted by aligning miRNAs to the transcriptome, and the list was reduced to include the intersection of hits found using the Miranda, PITA, and TargetScan algorithms. To further reduce false positives, putative targets were validated by cross-checking them to mRNAs reported in recent DENV2 host response transcriptome reports; 4076 targets were identified. Of these, 464 gene targets have predicted miRNA binding sites in 3′UTRs. Context-specific target functional groups include proteins involved in transport, transcriptional regulation, mitochondrial function, chromatin modification and signal transduction processes known to be required for viral replication and dissemination. The miRNA response is placed in context with other vector host response studies by comparing the predicted targets to those of transcriptome studies. Together, these data are consistent with the hypothesis that profound and persistent changes to gene expression occur in DENV2-exposed mosquitoes.