Identification of targets of miR-138 in Neuro-2a and 293T cells by RNAseq

We previously showed that miR-138 can repress herpes simplex virus 1 (HSV-1) ICP0 expression by binding to ICP0 mRNA. However, in this study we found that miR-138 can also repress viral gene expression independent of ICP0. We did not find other confirmed viral targets of miR-138. Therefore we conducted these RNAseq experiments (in combination with PAR-CLIP experiments whose results are uploaded separately) to identify host targets of miR-138 in two cell lines to explain the ICP0-independent effects on HSV-1 gene expression. Overall design: We transfected Neuro-2a cells or 293T cells with a miR-138 mimic or a scrambled control mimic, and compared miR-138 transfected with control transfected cells. Three biological replicates for each condition.

我们既往研究证实，微小RNA-138（miR-138）可通过结合单纯疱疹病毒1型（HSV-1）感染细胞蛋白0（ICP0）的信使RNA（mRNA），抑制该病毒ICP0的表达。但本研究发现，miR-138还可通过不依赖ICP0的途径抑制病毒基因的表达。我们未发现miR-138的其他经验证的病毒靶标。为此，我们开展了本次RNA测序（RNA-seq）实验（结合结果另行上传的光活性增强核苷酸交联免疫沉淀（PAR-CLIP）实验），在两种细胞株中鉴定miR-138的宿主靶标，以阐明其对HSV-1基因表达的不依赖ICP0的调控作用。实验设计概述：我们将miR-138模拟物或无序对照模拟物分别转染至Neuro-2a细胞与293T细胞，对比转染miR-138模拟物与转染对照模拟物的细胞样本，每组设置3次生物学重复。