Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, Wenjiang District, Chengdu, 611130, China.
Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, Wenjiang District, Chengdu, 611130, China.
BMC Genomics. 2022 Jul 14;23(1):509. doi: 10.1186/s12864-022-08739-7.
Duck plague virus (DPV), belonging to herpesviruses, is a linear double-stranded DNA virus. There are many reports about the outbreak of the duck plague in a variety of countries, which caused huge economic losses. Recently, increasing reports revealed that multiple long non-coding RNAs (lncRNAs) can possess great potential in the regulation of host antiviral immune response. Furthermore, it remains to be determined which specific molecular mechanisms are responsible for the DPV-host interaction in host immunity. Here, lncRNAs and mRNAs in DPV infected duck embryonic fibroblast (DEF) cells were identified by high-throughput RNA-sequencing (RNA-seq). And we predicted target genes of differentially expressed genes (DEGs) and formed a complex regulatory network depending on in-silico analysis and prediction.
RNA-seq analysis results showed that 2921 lncRNAs were found at 30 h post-infection (hpi). In our study, 218 DE lncRNAs and 2840 DE mRNAs were obtained in DEF after DPV infection. Among these DEGs and target genes, some have been authenticated as immune-related molecules, such as a Macrophage mannose receptor (MR), Anas platyrhynchos toll-like receptor 2 (TLR2), leukocyte differentiation antigen, interleukin family, and their related regulatory factors. Furthermore, according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis, we found that the target genes may have important effects on biological development, biosynthesis, signal transduction, cell biological regulation, and cell process. Also, we obtained, the potential targeting relationship existing in DEF cells between host lncRNAs and DPV-encoded miRNAs by software.
This study revealed not only expression changes, but also the possible biological regulatory relationship of lncRNAs and mRNAs in DPV infected DEF cells. Together, these data and analyses provide additional insight into the role of lncRNAs and mRNAs in the host's immune response to DPV infection.
鸭瘟病毒（DPV）属于疱疹病毒科，是一种线性双链 DNA 病毒。有许多关于在多个国家爆发鸭瘟的报道，这给养鸭业造成了巨大的经济损失。最近，越来越多的报道表明，多种长非编码 RNA（lncRNA）在宿主抗病毒免疫反应的调控中具有巨大潜力。此外，DPV 与宿主相互作用在宿主免疫中具体的分子机制仍有待确定。在这里，通过高通量 RNA 测序（RNA-seq）鉴定了 DPV 感染鸭胚胎成纤维细胞（DEF）细胞中的 lncRNA 和 mRNAs。并且，我们通过计算机分析和预测，预测了差异表达基因（DEGs）的靶基因，并形成了一个复杂的调控网络。
RNA-seq 分析结果表明，在感染后 30 小时（hpi）发现了 2921 个 lncRNA。在我们的研究中，DPV 感染 DEF 后获得了 218 个 DE lncRNA 和 2840 个 DE mRNA。在这些 DEGs 和靶基因中，有一些已被证实是与免疫相关的分子，如巨噬细胞甘露糖受体（MR）、鸭源 toll 样受体 2（TLR2）、白细胞分化抗原、白细胞介素家族及其相关调节因子。此外，根据京都基因与基因组百科全书（KEGG）和基因本体论（GO）富集分析，我们发现靶基因可能对生物发育、生物合成、信号转导、细胞生物学调节和细胞过程有重要影响。此外，我们还通过软件获得了 DEF 细胞中宿主 lncRNA 与 DPV 编码的 miRNA 之间存在的潜在靶向关系。
本研究不仅揭示了 DPV 感染 DEF 细胞中 lncRNA 和 mRNAs 的表达变化，还揭示了它们可能的生物学调控关系。这些数据和分析为 lncRNA 和 mRNAs 在宿主对 DPV 感染的免疫反应中的作用提供了更多的见解。
