Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus.
Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus.
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鸭瘟病毒感染鸭胚胎成纤维细胞中长链非编码RNA和mRNA的差异表达谱及计算机功能分析
DOI：
10.1186/s12864-022-08739-7
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发表时间：
2022-07-14
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
鸭瘟病毒（DPV）属于疱疹病毒属，是一种线性双链DNA病毒。关于鸭瘟在世界各国的爆发有很多报道，造成了巨大的经济损失。近年来，越来越多的研究表明，多个长链非编码RNA（lncRNA）在调节宿主抗病毒免疫应答中具有巨大的潜力。此外，还有待确定哪些特定的分子机制是负责DPV-宿主相互作用的宿主免疫。在此，通过高通量RNA测序（RNA-seq）鉴定DPV感染的鸭胚胎成纤维细胞（DEF）中的lncRNA和mRNA。通过计算机模拟分析和预测，预测了差异表达基因的靶基因，形成了一个复杂的调控网络。RNA-seq分析结果显示，在感染后30 h（hpi）发现2921个lncRNA。在我们的研究中，在DPV感染后的DEF中获得了218个DE lncRNA和2840个DE mRNAs。在这些DEG和靶基因中，一些已被证实为免疫相关分子，如巨噬细胞甘露糖受体（MR）、绿头鸭toll样受体2（TLR 2）、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）的富集分析，我们发现目的基因可能在生物发育、生物合成、信号转导、细胞生物学调节和细胞过程中发挥重要作用。通过软件分析，获得了宿主lncRNA与DPV编码的miRNAs在DEF细胞中存在的潜在靶向性关系。本研究不仅揭示了DPV感染DEF细胞后lncRNA和mRNAs的表达变化，而且揭示了它们之间可能的生物学调控关系。总之，这些数据和分析为lncRNA和mRNA在宿主对DPV感染的免疫应答中的作用提供了额外的见解。在线版本包含补充材料，可通过10.1186/s12864-022-08739-7获得。
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. The online version contains supplementary material available at 10.1186/s12864-022-08739-7.
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影响因子：
8
作者：
Braconi, C.;Kogure, T.;Valeri, N.;Huang, N.;Nuovo, G.;Costinean, S.;Negrini, M.;Miotto, E.;Croce, C. M.;Patel, T.
通讯作者：
Patel, T.
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
鸭天宝苏病毒感染鸭胚胎成纤维细胞中长链非编码RNA的差异表达分析及功能预测
影响因子：
7.3
作者：
Lin, Yun;Yang, Jing;Diao, Youxiang
通讯作者：
Diao, Youxiang
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.