Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing

Abstract

Porcine circovirus-associated disease (PCVAD), which is induced by porcine circovirus type 2 (PCV2), is responsible for severe economic losses. Recently, the role of noncoding RNAs, and in particular microRNAs, in PCV2 infection has received great attention. However, the role of long noncoding RNA (lncRNA) in PCV2 infection is unclear. Here, for the first time, we describe the expression profiles of lncRNAs in an intestinal porcine epithelial cell line (IPEC-J2) after PCV2 infection, and analyze the features of differently expressed lncRNAs and their potential target genes. After strict filtering of approximately 150 million reads, we identified 13,520 lncRNAs, including 199 lncRNAs that were differentially expressed in non-infected and PCV2-infected cells. Furthermore, trans analysis found lncRNA-regulated target genes enriched for specific Gene Ontology terms (P < 0.05), such as DNA binding, RNA binding, and transcription factor activity, which are closely associated with PCV2 infection. In addition, we analyzed the predicted target genes of differentially expressed lncRNAs, including SOD2, TNFAIP3, and ARG1, all of which are involved in infectious diseases. Our study identifies many candidate lncRNAs involved in PCV2 infection and provides new insight into the mechanisms underlying the pathogenesis of PCVAD.

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

“…HIV, porcine circovirus 2, HSV-1, rabies virus, avian leukosis virus J, bovine viral diarrhea virus) and parasites (e.g. Echinococcus granulosus, Cryptosporidium parvum, Cryptosporidium baileyi) in animals and humans [28,33,[66][67][68][69][70][71][72][73]. The expression profiles of host circRNAs were also elucidated after infections of avian leukosis virus J [74], bovine viral diarrhea virus [75], human cytomegalovirus [76], Orf virus [30], porcine endemic diarrhea virus [29], HIV [77], transmissible gastroenteritis virus [78], Mycobacterium tuberculosis [79], Clostridium perfringens [80] and C. baileyi [33].…”

Identification of lncRNAs Involved in PCV2 Infection of PK-15 Cells

“…Direct quantifications of the protein amounts after PCV2 infection revealed that there were altered levels of cytoskeletal proteins, stress response proteins, signal transduction proteins, and proteins involved in the ubiquitin-proteasome processes [ 32 , 51 ]. However, only one study had previously been performed to evaluate the effect of lncRNAs on PCV2 infection [ 25 ]. Fang et al used PCV2 to infect the porcine intestinal epithelial cell line IPEC-J2 to mimic porcine enteritis.…”

“…However, they used the p -value instead of the adjusted p -value to identify the altered lncRNAs and mRNAs, which would substantially increase the type I error, leading to false positive findings. For example, in their lncRNA list, no lncRNA identified has an adjusted p -value of less than 0.05 [ 25 ]. Therefore, in the current study, we aimed to study whether some differentially expressed lncRNAs could be found using more stringent screening parameters.…”

“…Next, differentially expressed transcripts were calculated based on the following parameters: |log 2 fold change| > 0.2630 (fold change greater than 1.2 or lesser than 5/6) and adjusted p -value (false discovery rate, FDR) < 0.05 using the DESeq2 tool [ 36 ]. The identification of lncRNAs used a strategy described in a previous report [ 25 ]. The sequenced reads were submitted to the Gene Expression Omnibus with the accession number: GSE149711.…”

“…Since their discovery, lncRNAs have been implicated in numerous biological processes, including cell signaling [ 18 ], epigenetic regulation [ 19 ], enhancer trapping [ 20 ], human diseases [ 21 , 22 ], and virus-host interactions [ 23 , 24 ]. However, until recently, only one study regarding the effect of lncRNAs on PCV2 infection has been published, in which the lncRNA-regulated mRNAs were found to be enriched in the DNA/RNA binding, transcription factor activity, immune response, the MAPK (mitogen-activated protein kinase) signaling pathway, and cytokine–cytokine receptor interaction [ 25 ].…”