Integrative analysis of microRNA and mRNA expression profiles in MARC-145 cells infected with PRRSV
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ORIGINAL PAPER
Integrative analysis of microRNA and mRNA expression profiles in MARC‑145 cells infected with PRRSV Zhenpu Liang1 · Liang Wang1 · Hui Wu1 · Deepali Singh2 · Xiaoxia Zhang1 Received: 8 April 2020 / Accepted: 5 August 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) causes tremendous economic losses to the swine industry worldwide. miRNAs are crucial regulators of gene expression and a wide range of complex interactions of miRNAs–mRNAs is possible during virus infection. However, there is no comprehensive integrated study of miRNA and mRNA networks in MARC-145 cells after infection with PRRSV. We analyzed the differential expressions, co-relations, annotations, and putative functions of miRNA and mRNA networks in PRRSV-infected MARC-145 cells. Based on the filtering criterion, 22 differentially expressed miRNAs (DEmiRs) (15 up- and 7 downregulated) were filtered out. miRNA–mRNA interaction networks were constructed. For the 18 selected miRNAs, 390 potential target genes were predicted from the differentially expressed mRNAs (DEmRs). GO and KEGG pathway annotations predicted 34 KEGG pathways, 12 of which are known to be involved in virus infection. Real-time PCR validated the RNA-seq results. Our analysis showed that miR-27a-5p and miR-21-3p downregulate the expression of two of their potential target genes–SPARC, CLIC1, and cofilin-1, COX7A2, respectively. Further experiments proved that miR-21-3p and miR-27a-5p can promote PRRSV replication significantly. It is the first report that these two miRNAs participate in the interaction of host cells with PRRSV. Our results provide insights into the role of miRNAs in response to PRRSV infection, which will aid the research for developing novel therapies against PRRSV. Keywords Integrated analysis · miRNA · mRNA · PRRSV · MARC-145
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11262-020-01786-w) contains supplementary material, which is available to authorized users. * Xiaoxia Zhang [email protected] Zhenpu Liang [email protected] Liang Wang [email protected] Hui Wu [email protected] Deepali Singh [email protected] 1
College of Life Sciences, Henan Agricultural University, Zhengzhou 450000, China
School of Biotechnology, Gautam Buddha University, Greater Noida 201312, India
2
Porcine reproductive and respiratory syndrome virus (PRRSV), a member of the Arteriviridae family, is an enveloped, positive-strand RNA virus. PRRSV is the etiologic agent of PRRS which can cause reproductive failure in pregnant sows and may cause a persistent respiratory disturbance, particularly to piglets [1]. Worldwide, this virus has brought tremendous economic losses to the swine industry [2, 3]. PRRSV replicates in the porcine macrophages, in which it can establish a chronic infection. MARC-145, a monkey kidney cell line, has been extensively used to study PRRSV infection and life cycle [4–6]. Previous reports
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