Expression Profile Changes Of MRNA And LncRNA And Their Function Prediction In ST Cells After TGEV Infection

Pig diarrhea is one of the most prominent diseases restricting the healthy development of swine industry in our country,and transmissible gastroenteritis virus(TGEV)caused diarrhea,namely porcine transmissible gastroenteritis(TGE)is of wide prevalences and great harm.However,to date,prevention and control effectiveness of TGE is still not ideal,due to the lack of adequate understanding of TGEV infection mechanism and the interactions between pathogen and host.Long non-coding RNA,a new class of molecules with important biological function,closely related to cell differentiation,development and disease,represents a hot topic in life science.However,it has not known if lncRNA plays a role in pathogenesis of TGEV infection,and little is known about the response and mechanism of host functional genes after TGEV infection.Therefore,the present study aimed to use swine testicle cells as experimental material,using high-throughput sequencing technology to reveal TGEV infection induced ST cells mRNA/lncRNA expression profile,mining the differentially expressed mRNA/lncRNA,and to predicte functions of differentially expressed mRNA/lncRNA during the infection process by means of bioinformatics analysis,trying to explore response and mechanisms of ST cells against TGEV from mRNA/lncRNA level.In this study,RNA-seq was used to quantitatively identify differentially expressed mRNAs and lncRNAs at early(6h post infection)and late(48h post infection)stage in TGEV-infected ST cells.We identified 436 differentially expressed mRNAs in early stage,388 of them were up regulated,48 mRNAs were down regulated.In late stage,there were 308 mRNAs expressed differentially,182 of them were up regulated,126 mRNAs were down regulated.GO and KEGG pathway enrichment analysis of the differentially expressed mRNAs showed that multiple biological processes,such as TNF signaling pathway,phagosome and lysosome activation,were enriched in early stage of TGEV infection.While in late stage,the differentially expressed genes were enriched in toll-like receptor signaling pathway and NOD-like receptor signaling pathway and apoptosis signaling pathway et al.Then,the mRNAs expression in toll-like receptor signaling pathway were analysised by quantitative real-time PCR together with RNA-seq database,the result indicated that TGEV activated the TLR3 signaling pathway and therefore increased IFN-β level in vitro.Otherwise,23 differentially expressed lncRNAs were indentified in early infection stage,15 of them were up regulated,8 of them were down regulated.In late stage,there were 67 lncRNAs expressed differentially,7 of them were up regulated,60 of them were down regulated.25 differentially expressed lncRNAs were selected randomly to predict their target genes,the result showed that 7 lncRNAs have target genes with trans interaction.Among the 7 lncRNAs,lncRNA LOC100524077 was identify to regulate the expression of SPP1 and PKD2 which were differentially expressed when ST cells were infected by TGEV.Hence,lncRNA LOC100524077 was assumed to play an important role in cell immunity,survival and cation transportation.In addition,our study also indentified 8142 new lncRNAs with 8 of them were differentially expressed.As the function of these new lncRNAs remains unclear yet,we will focus on it in future study.Taken together,the current study reveal that TGEV infection could induce huge number of mRNAs and lncRNAs to differentially expressed both in early and late stage;TLR3 signaling pathway was activated in late stage of TGEV infection;lncRNA LOC100524077 may influence cell immunity,survival and cation transportation by regulating SPP1 and PKD2 expression.