Abstract
BackgroundAvian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections. However, little is known about the function of lncRNAs in host cultured cells in response to IBV infection.ResultsWe used next-generation high throughput sequencing to reveal the expression profiles of mRNAs and lncRNAs in IBV-infected HD11 cells. Compared with the uninfected cells, we identified 153 differentially expressed (DE) mRNAs (106 up-regulated mRNAs, 47 down-regulated mRNAs) and 181 DE lncRNAs (59 up-regulated lncRNAs, 122 down-regulated lncRNAs) in IBV-infected HD11 cells. Moreover, gene ontology (GO) and pathway enrichment analyses indicated that DE mRNAs and lncRNAs were mainly involved in cellular innate immunity, amino acid metabolism, and nucleic acid metabolism. In addition, 2640 novel chicken lncRNAs were identified, and a competing endogenous RNA (ceRNAs) network centered on gga-miR-30d and miR-146a-5p was established.ConclusionsWe identified expression profiles of mRNAs and lncRNAs during IBV infection that provided new insights into the pathogenesis of IBV.
Highlights
Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide
We have previously analyzed the miRNAs of IBV-infected chicken kidney tissue and obtained two differentially expressed miRNAs, namely gga-miR-30d and miR-146a5p, which are encoded by chicken chromosomes 1 and 13, respectively [15]
Replication status of IBV in HD11 cells The expression of non-coding RNAs in cells is closely related to the stage of virus infection [13]
Summary
Replication status of IBV in HD11 cells The expression of non-coding RNAs (ncRNAs) in cells is closely related to the stage of virus infection [13]. To predict the trans-regulated target genes of lncRNAs, the top 10 DE lncRNAs and 50 most relevant mRNAs were selected to construct the co-expression network of lncRNA–mRNA pairs based on Pearson’s correlation coefficient by Cytoscape (Additional File 4). Expression profiles of lncRNAs and mRNAs in IBV-infected HD11 cells In total, we obtained 15,358 mRNAs and 11,510 lncRNAs. 153 mRNAs were differentially expressed, with 106 mRNAs significantly up-regulated and 47 mRNAs significantly down-regulated (Additional File 1). Heat map and M-A map enrichment analyses (Fig. 4) revealed that compared with the control group, the expression profiles of lncRNAs and mRNAs changed significantly after 36 h of IBV infection. We screened the DEGs related to innate immunity in HD11 cells infected with IBV for 36 h These genes included CSF2, IFIT5, IL15, IL1RAPL1, IL22, IL8, MX1, NR1H4, S100A9, SYK, TRAF5, TRIM67, and ZFPM2.
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