Genome-wide analysis of simian virus 40 infected cells

The goal of this study was to compare the whole transcriptional profile (RNA-seq) of simian virus 40 infection and mock infected Vero cells at 72 hours post infection. Circular RNAs (circRNAs), identified as a class of widely expressed endogenous regulatory RNAs, are involved in diverse physiological and pathological processes. However, their role in viral pathogenesis and cellular antiviral response remains unexplored. In this study, a potent DNA tumor virus, simian virus 40 (SV40), was used as a model to investigate the viral influences on cellular circRNA transcriptome. Using RNA-seq, 15,241 putative circRNAs were identified de novo from 5,057 parental genes in monkey kidney–derived Vero cells. The expression of selected circRNAs was confirmed by reverse transcription-polymerase chain reaction and Sanger sequencing. Further analysis showed that most circRNAs comprised multiple exons, and most parental genes produced multiple circRNA isoforms. A total of 134 significantly dysregulated circRNAs, including 103 upregulated and 31 downregulated circRNAs, were found after SV40 infection. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that various cancer-related pathways, including p53 and Wnt pathway, could be affected by SV40 infection via the alteration of the circRNA hosting genes. Moreover, diverse cellular immune pathways, including Toll-like receptor pathway and Janus kinase–signal transducer and activator of transcription pathway, could also be affected by SV40 infection. An integrated circRNA-miRNA-gene analysis suggested the putative function of circRNAs as cellular and viral miRNA decoys to indirectly regulate the gene expression during SV40 infection. This study presented the first comprehensive expression and functional profile of circRNAs in response to SV40 infection, thus providing new insights into the mechanisms of viral pathogenesis and cellular immune response. Overall design: Whole transcriptome profiles of simian virus 40 infection and mock infected Vero cells at 72 hours post infection were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000 platform.