Porcine endemic diarrhea virus infection regulates long noncoding RNA expression

Abstract

Long noncoding RNAs (lncRNAs) have been implicated in various life processes. However, the lncRNA expression and potential functions in porcine endemic diarrhea virus (PEDV) infection and host defense are still poorly understood. In this study, we investigated the lncRNA expression profiles during PEDV infection in intestinal porcine epithelial cell-jejunum 2 (IPEC-J2) cell lines by next-generation sequencing and identified 6188 novel lncRNAs. The functional annotation analysis revealed that these lncRNAs might be associated with many immunity-related genes. We next selected candidate lncRNAs related to immune response pathways and further identified their differential expression in PEDV-infected IPEC-J2 cells and newborn piglets. Our results demonstrated that PEDV infection regulated lncRNA expression patterns in both the IPEC-J2 cell line and piglet ileum. These findings provide the first large-scale survey of lncRNAs associated with PEDV infection, specifically the lncRNAs responsible for the activation of the immune system within the ileum.

Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection

“…These lncRNAs were characterized by shorter transcript length, longer exons, lower estimated number of exons and lower expression levels. These properties were also observed in other reported lncRNAs within the genome [20,[35][36][37].…”

“…LncRNAs have been reported to be involved in the coronavirus infections [20,34], but the roles of lncRNAs during TGEV induced inflammation response have not yet been elucidated. In our study, NGS techniques were used to investigate the lncRNA expression profiles of TGEV infected IPEC-J2.…”

“…The potential functions of differentially expressed mRNAs, miRNAs and circRNAs were anlyzed and were closely related to inflammatory response [16]. Recently, increasing studies have indicated that lncRNAs play important roles in inflammatory response [17][18][19][20]. Therefore, we proposed that lncRNAs also might participate in regulating inflammatory response during TGEV infection.…”

Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection

“…To explore the function of PML in the process of TGEV induced NF-κB activation, The siRNA of PML (si-PML-1 and si-PML-2 or negative control) were transfected into IPEC-J2 cells respectively , then infected with TGEV at 1 MOI for 24 h. The PML level was down-regulated by si-PML-1 and not affected by si-PML-2 (Fig 9d). p-p65 was decreased by si-PML-1 and not affected by si-PML-2 (Fig 9e).The siRNA sequences were shown in Additional file 9: Table S9 Discussion Recent studies have shown that lncRNAs play important roles during antiviral innate immune response [16][17][18][19]. In particular, lncRNAs have been reported to be involved in the coronavirus infections [19,33], but the roles of lncRNAs during TGEV induced innate immune response have not yet been elucidated.…”

“…We also predicted potential functions of differentially expressed mRNAs, miRNAs and circRNAs that were closely related to inflammatory and immune response [15]. Recently, increasing studies have indicated that lncRNAs play important roles during antiviral innate immune response [16][17][18][19]. A recent study has shown that PEDV infection regulated lncRNAs expression patterns in the IPEC-J2 cell line, and lncRNAs may be involved in PEDV induced innate immune response by their host genes.…”