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. 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.

为分析传染性胃肠炎病毒（Transmissible gastroenteritis virus, TGEV）感染对猪肾上皮细胞系（PK-15）环状RNA（circular RNAs, circRNAs）表达谱的影响，本研究基于Illumina HiSeq 4000测序平台，对对照组及TGEV感染的PK-15细胞开展circRNAs转录组测序。对差异表达circRNAs（differentially expressed circRNAs, DE circRNAs）的源基因进行GO功能富集分析（Gene Ontology, GO）及KEGG通路富集分析（Kyoto Encyclopedia of Genes and Genomes, KEGG）。同时，构建DE circRNAs的调控网络，并预测多条与先天性免疫及TGEV致病机制相关的circRNA-miRNA-mRNA调控轴。本研究的转录组测序结果显示，在对照组与TGEV感染的PK-15细胞中共鉴定出1029种新型circRNAs。与对照组PK-15细胞相比，TGEV感染的PK-15细胞中有70种circRNAs表达显著上调，58种circRNAs表达显著下调。对DE circRNAs的源基因进行GO功能分析结果表明，TGEV感染的PK-15细胞中DE circRNAs的源基因主要富集于细胞内组分、细胞内膜结合细胞器及细胞核，同时涉及细胞大分子代谢过程、含氮碱基化合物代谢过程、含氮化合物代谢过程、细胞代谢过程调控，以及杂环化合物结合、有机环化合物结合与核酸结合等功能条目。KEGG通路富集分析结果显示，TGEV感染的PK-15细胞中DE circRNAs的源基因主要富集于肌动蛋白细胞骨架调控、甲型流感、丙型肝炎及cAMP信号通路。circRNA-miRNA-mRNA互作网络分析显示，circRNAs可调控先天性免疫与跨膜离子转运过程。为探究circRNAs在TGEV感染过程中的潜在调控作用，本研究通过用TGEV感染PK-15细胞构建TGEV感染细胞模型。对TGEV感染细胞模型及正常PK-15细胞进行RNA测序，每个样本设置3次独立生物学重复。从测序数据中分析并筛选DE circRNAs，对其源基因开展GO功能及KEGG通路富集分析，最终通过生物信息学方法预测并验证与病毒感染宿主免疫相关的circRNA-miRNA-mRNA调控轴。