传染性法氏囊病病毒感染DF-1细胞的lncRNA表达谱变化分析
|
摘要
传染性法氏囊病(Infectious bursal disease, IBD)是一种由传染性法氏囊病病毒(Infectious bursal disease virus, IBDV)引起的急性、高度接触性的传染病,在易感雏鸡(Gallus gallus)群中发病率可达80%～100%,死亡率高达30%～35%。为探究IBDV感染所引起的宿主细胞内长链非编码RNA (long noncoding RNA, lncRNA)表达谱变化,本研究利用Illumina Hiseq 3000平台进行高通量测序,并对IBDV感染和未感染的鸡成纤维细胞系DF-1的lncRNA表达谱进行分析。结果显示,有958条差异表达的lncRNA,其中728条上调、230条下调。利用miRanda-aug2010软件预测差异lncRNA的靶基因,然后通过生物信息学方法对靶基因进行基因本体论(Gene Oncology, GO)注释和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes, KEGG)信号通路富集分析,结果显示,靶基因在免疫应答过程、细胞因子反应、细胞凋亡和核因子κB (nuclear factorκB, NF-κB)等生物学过程中显著富集,参与视黄酸诱导基因蛋白Ⅰ(retinoic acid-inducible geneⅠ, RIG-Ⅰ)信号通路、Toll样受体信号通路和细胞凋亡等通路。利用qRT-PCR方法对随机挑选的9条lncRNA进行验证,结果显示,其表达变化趋势与高通量测序数据一致。本研究对IBDV lncRNA表达谱进行分析,为深入探讨与IBDV发病机制相关的关键lncRNA分子作用机制提供了参考依据。
Infectious bursal disease(IBD) is an acute, highly contagious infectious disease caused by Infectious bursal disease virus(IBDV). The incidence rate of IBD in susceptible young chickens(Gallus gallus)can reach 80%～100%, and the mortality rate is as high as 30%～35%. To test the changes of long noncoding RNA(lncRNA) in host cells infected with IBDV, the expression profile of lncRNA in IBDV-infected and mock-infected chicken fibroblast line DF-1 cells were analyzed by high throughput sequencing. The results showed that there were 958 differentially expressed lncRNA. Among them, 728 were up-regulated and 230 were down-regulated. Target genes of the differentially expressed lncRNA were predicted. Functional annotation or enrichment analysis was performed by Gene Oncology(GO) or Kyoto Encyclopedia of Genes and Genomes(KEGG). GO analysis suggested that target genes of the differentially expressed lncRNA involved in immune response, cell death, response to cytokine and I-κB kinase/NF-κB signaling. KEGG enrichment analysis suggested that these genes functioned in various cellular signaling pathways, including Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and apoptosis. Differentially expression of 9 randomly selected lncRNAs were verified by real-time quantitative polymerase chain reaction(qRT-PCR). The results were consistent with high throughput sequencing data. This is the first report of the differentially expression of lncRNA in DF-1 cells upon IBDV infection. This study provides a basis for further research on key lncRNA related to the host immunity and IBDV pathogenesis.
Infectious bursal disease(IBD) is an acute, highly contagious infectious disease caused by Infectious bursal disease virus(IBDV). The incidence rate of IBD in susceptible young chickens(Gallus gallus)can reach 80%～100%, and the mortality rate is as high as 30%～35%. To test the changes of long noncoding RNA(lncRNA) in host cells infected with IBDV, the expression profile of lncRNA in IBDV-infected and mock-infected chicken fibroblast line DF-1 cells were analyzed by high throughput sequencing. The results showed that there were 958 differentially expressed lncRNA. Among them, 728 were up-regulated and 230 were down-regulated. Target genes of the differentially expressed lncRNA were predicted. Functional annotation or enrichment analysis was performed by Gene Oncology(GO) or Kyoto Encyclopedia of Genes and Genomes(KEGG). GO analysis suggested that target genes of the differentially expressed lncRNA involved in immune response, cell death, response to cytokine and I-κB kinase/NF-κB signaling. KEGG enrichment analysis suggested that these genes functioned in various cellular signaling pathways, including Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and apoptosis. Differentially expression of 9 randomly selected lncRNAs were verified by real-time quantitative polymerase chain reaction(qRT-PCR). The results were consistent with high throughput sequencing data. This is the first report of the differentially expression of lncRNA in DF-1 cells upon IBDV infection. This study provides a basis for further research on key lncRNA related to the host immunity and IBDV pathogenesis.
引文
Burgler C,Macdonald P M.2005.Prediction and verification of microRNA targets by MovingTargets,a highly adaptable prediction method[J].BioMed Central Genomics,6(1):88.
Chai W J,Li J,Shangguan Q L,et al.2018.Lnc-ISG20 inhibits Influenza A virus replication by enhancing ISG20 expression[J].Journal of Virology,92(16):e00539-18.
Deng L,Yang S B,Xu F F,et al.2015.Long noncoding RNACCAT1 promotes hepatocellular carcinoma progression by functioning as let-7 sponge[J].Journal of Experimental and Clinical Cancer Research,34(1):1-10.
Dobos P,Hill B J,Hallett R,et al.1979.Biophysical and biochemical characterization of 5 animal viruses with bisegmented double-stranded RNA genomes[J].Journal of Virology,32(2):593-605.
Fabrício F.Costa.2010.Non-coding RNAs:Meet thy masters[J].Bioessays News and Reviews in Molecular Cellular and Developmental Biology,32(7):599-608.
Heward J A,Lindsay M A.2014.Long non-coding RNAs in the regulation of the immune response[J].Trends in Immunology,35(9):408-419.
Lewis B P,Burge C B,Bartel D P.2005.Conserved seed pairing,often flanked by adenosines,indicates that thousands of human genes are microRNA targets[J].Cell,120(1):15-20.
Li L,Huang Y W,Wang L S,et al.2010.Synthesis of reassortant infectious Bursal disease virus in chickens injected directly with infectious clones from different virus strains[J].Acta Biochimica Et Biophysica Sinica,37(3):192-198.
Mercer T R,Dinger M E,Mattick J S.2009.Long non-coding RNAs:Insights into functions[J].Nature Reviews Genetics,10(3):155-159.
Müller H,Islam M R,Raue R.2003.Research on infectious bursal disease-the past,the present and the future[J].Veterinary Microbiology,97(1):153-165.
Ouyang J,Zhu X,Chen Y,et al.2014.NRAV,a long noncoding RNA,modulates antiviral responses through suppression of interferon-stimulated gene transcription[J].Cell Host and Microbe,16(5):616-626.
Rui X,Xu Y,Jiang X,et al.2018.Long non-coding RNAC5orf66-AS1 promotes cell proliferation in cervical cancer by targeting miR-637/RING1 axis[J].Cell Death and Disease,9(12):1175.
Saminathan S,Yongsam J,Luhua T,et al.2018.Genomewide identification,functional prediction and expression profiling of long non-coding RNAs in Camelina sativa[J].Plant Growth Regulation,86(1):49-63.
Satpathy A,Chang H.2015.Long noncoding RNA in hematopoiesis and immunity[J].Immunity,42(5):792-804.
Shannon P,Markiel A,Ozier O,et al.2003.Cytoscape:A software environment for integrated models of biomolecular interaction networks[J].Genome Research,13(11):2498-2504.
Szcze?niak M W,Maka?owska I.2016.IncRNA-RNA interactions across the human transcriptome[J].PLoS One,11(3):e0150353.
Vakharia V N,He J,Ahamed B,et al.1994.Molecular basis of antigenic variation in infectious Bursal disease virus[J].Virus Research,31(2):265-273.
Zhao P S,Liu S D,Zhong Z X,et al.2018.Analysis of expression profiles of long noncoding RNAs and mRNAs in brains of mice infected by rabies virus by RNA sequencing[J].Scientific Reports,8(1):11858.
Zhang Y,Gao X T.2016.Long noncoding RNAs in innate immunity[J].Cellular and Molecular Immunology,13(2):138-147.
Chai W J,Li J,Shangguan Q L,et al.2018.Lnc-ISG20 inhibits Influenza A virus replication by enhancing ISG20 expression[J].Journal of Virology,92(16):e00539-18.
Deng L,Yang S B,Xu F F,et al.2015.Long noncoding RNACCAT1 promotes hepatocellular carcinoma progression by functioning as let-7 sponge[J].Journal of Experimental and Clinical Cancer Research,34(1):1-10.
Dobos P,Hill B J,Hallett R,et al.1979.Biophysical and biochemical characterization of 5 animal viruses with bisegmented double-stranded RNA genomes[J].Journal of Virology,32(2):593-605.
Fabrício F.Costa.2010.Non-coding RNAs:Meet thy masters[J].Bioessays News and Reviews in Molecular Cellular and Developmental Biology,32(7):599-608.
Heward J A,Lindsay M A.2014.Long non-coding RNAs in the regulation of the immune response[J].Trends in Immunology,35(9):408-419.
Lewis B P,Burge C B,Bartel D P.2005.Conserved seed pairing,often flanked by adenosines,indicates that thousands of human genes are microRNA targets[J].Cell,120(1):15-20.
Li L,Huang Y W,Wang L S,et al.2010.Synthesis of reassortant infectious Bursal disease virus in chickens injected directly with infectious clones from different virus strains[J].Acta Biochimica Et Biophysica Sinica,37(3):192-198.
Mercer T R,Dinger M E,Mattick J S.2009.Long non-coding RNAs:Insights into functions[J].Nature Reviews Genetics,10(3):155-159.
Müller H,Islam M R,Raue R.2003.Research on infectious bursal disease-the past,the present and the future[J].Veterinary Microbiology,97(1):153-165.
Ouyang J,Zhu X,Chen Y,et al.2014.NRAV,a long noncoding RNA,modulates antiviral responses through suppression of interferon-stimulated gene transcription[J].Cell Host and Microbe,16(5):616-626.
Rui X,Xu Y,Jiang X,et al.2018.Long non-coding RNAC5orf66-AS1 promotes cell proliferation in cervical cancer by targeting miR-637/RING1 axis[J].Cell Death and Disease,9(12):1175.
Saminathan S,Yongsam J,Luhua T,et al.2018.Genomewide identification,functional prediction and expression profiling of long non-coding RNAs in Camelina sativa[J].Plant Growth Regulation,86(1):49-63.
Satpathy A,Chang H.2015.Long noncoding RNA in hematopoiesis and immunity[J].Immunity,42(5):792-804.
Shannon P,Markiel A,Ozier O,et al.2003.Cytoscape:A software environment for integrated models of biomolecular interaction networks[J].Genome Research,13(11):2498-2504.
Szcze?niak M W,Maka?owska I.2016.IncRNA-RNA interactions across the human transcriptome[J].PLoS One,11(3):e0150353.
Vakharia V N,He J,Ahamed B,et al.1994.Molecular basis of antigenic variation in infectious Bursal disease virus[J].Virus Research,31(2):265-273.
Zhao P S,Liu S D,Zhong Z X,et al.2018.Analysis of expression profiles of long noncoding RNAs and mRNAs in brains of mice infected by rabies virus by RNA sequencing[J].Scientific Reports,8(1):11858.
Zhang Y,Gao X T.2016.Long noncoding RNAs in innate immunity[J].Cellular and Molecular Immunology,13(2):138-147.