circRNA Expression Profiling Analysis of Transmissible Gastroenteritis Virus-infected PK-15 Cells
[Objective]This study was aimed to analyze the effects of Transmissible gastroenteritis virus(TGEV)infection on circular RNA(circRNA)expression in porcine kidney epithelial cells(PK-15)and the potential regulatory functions of differentially expressed circRNA.[Method]Illumina HiSeq 4000 sequencing platform was used to sequence circRNA transcriptome of PK-15 cells(control)and TGEV-infected PK-15 cells,then screened differentially expressed circRNA.GO function and KEGG pathway enrichment analysis of differentially expressed circRNAs-derived genes were performed.TGEV infection-associated circRNA-miRNA-mRNA regulatory network was predicted.Moreover,12 differentially expressed circRNAs were randomly selected to verify their expression by Real-time quantitative PCR.[Result]Sequencing results revealed 1 029 novel circRNAs.Compared with PK-15 cells,a total of 128 significantly differentially expressed circRNAs were identified in TGEV-infected PK-15 cells,of which 70 circRNAs were upregulated and 58 circRNAs were downregulated.GO functional analysis showed that the genes originating from differentially expressed circRNAs in TGEV-infected PK-15 cells were mainly enriched in biological processes such as cellular macromolecular metabolic processes and cellular metabolism,cellular components such as intracellular fractions and intracellular membrane-bound organelles,and molecular functions such as organic ring compound binding and nucleic acid binding.KEGG pathway enrichment results showed that the differentially expressed circRNAs source genes in TGEV-infected PK-15 cells were mainly enriched in actin cytoskeleton regulation,influenza A,hepatitis C,cAMP signaling pathway,mTOR signaling pathway,etc.The circRNA-miRNA-mRNA regulatory network revealed that there was a large and complex circRNA regulatory network in TGEV-infected PK-15 cells,and a variety of circRNAs regulated innate immunity and transmembrane ion transport by targeting genes IFNAR1,IFNAR2 and NHE3 via miRNAs,thereby affecting TGEV infection and symptoms.Real-time quantitative PCR showed that the expression of 12 differentially expressed circRNAs were consistent with the basal trend of RNA-Seq results.[Conclusion]TGEV altered circRNA expression in PK-15 cells.Differentially expressed circRNA-derived genes were widely involved in cellular macromolecular metabolism,viral infection and cAMP signaling pathways.Multiple target genes IFNAR1,IFNAR2 and NHE3 associated with innate immunity and TGEV pathogenesis were regulated by circRNA.The results revealed the potential function of circRNA in TGEV-host interactions.
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