circRNAs expression profile analysis of PK-15 cells response to transmissible gastroenteritis virus infection
To analyze the effect of Transmissible gastroenteritis virus (TGEV) infection on expression profile of circular RNAs (circRNAs) in pig renal epithelial cells (PK-15), we decided to sequence the circRNAs transcriptome of control and TGEV-infected PK-15 cells based on the Illumina HiSeq 4000 platform. The source genes of the differentially expressed circRNAs were subjected to GO function and KEGG pathway enrichment analysis. Meanwhile, we built a regulatory network of DE circRNAs and predicted multiple circRNA-miRNA-mRNA regulatory axes about innate immunity and the pathogenesis of TGEV. In this study, transcriptome sequencing results revealed that a total of 1029 novel circRNAs were identified in the control and TGEV- infected PK -15 cells. In TGEV-infected PK-15 cells, the expression levels of 70 circRNAs were significantly up-regulated and 58 circRNAs were significantly down-regulated compared to control PK-15 cells. GO functional analysis of the source genes of differentially expressed circRNAs indicated that the differentially expressed circRNAs source genes in TGEV-infected PK-15 cells were mainly enriched in the intracellular part, intracellular membrane-bounded organelle and nucleus and cellular macromolecule metabolic process, nucleobase-containing compound metabolic process, nitrogen compound metabolic process, and regulation of cellular metabolic process and heterocyclic compound binding, organic cyclic compound binding and nucleic acid binding.The results of KEGG pathway enrichment analysis showed that the significantly differentially expressed circRNAs source genes in the TGEV-infected PK -15 cells were mainly enriched in the regulation of actin cytoskeleton, influenza A, hepatitis C and cAMP signaling pathway. circRNA-miRNA-mRNA interaction networks demonstrated that circRNAs regulated innate immunity and transmembrane ion transport. Overall design: To explore the potential regulatory role of circRNAs during Transmissible gastroenteritis virus(TGEV) infection. We established a TGEV infected cell model by infecting PK-15 cells with TGEV. RNA-seq was performed on TGEV infected cell models and PK-15 cells, with three independent replicates set for each sample. Analyze and screen differentially expressed circRNAs from sequencing data. The source genes of the differentially expressed circRNAs were subjected to GO function and KEGG pathway enrichment analysis. Finally, bioinformatics analysis was used to predict and validate the circRNA-miRNA-mRNA regulatory axis associated with host immunity in viral infections.