Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
复制标题
鸭（Anas platyrhynchos）响应 H5N1 流感病毒的长非编码 RNA 的鉴定和分析
DOI：
10.1186/s12864-018-5422-2
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发表时间：
2019-01-11
期刊：
影响因子：
4.4
通讯作者：
Huang, Yinhua
中科院分区：
文献类型：
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作者：
Lu, Chang;Xing, Yanling;Huang, Yinhua
背景长非编码RNA(Long Non-Coding RNAs，LncRNAs)是哺乳动物基因组的重要组成部分，其数量甚至超过蛋白质编码基因。例如，人类(96,308比20,376)和小鼠(87,774比22,630)在NONCODEv5数据库中拥有比蛋白质编码基因更多的lncRNA基因。最近，哺乳动物的lncRNAs被报道在甲型流感病毒感染的免疫应答中发挥重要作用。结果我们从人、小鼠、鸡、斑马鱼和线虫中筛选出62,447个与甲型流感病毒免疫应答相关的lncRNA，并结合转录数据建立了一条鉴定lncRNA的管道。然后，我们从来自三个组织的21个个体的RNA-Seq数据中收集了151,970个组装的转录本，并注释了4094个鸭的lncRNAs。与鸭蛋白的转录本比较，发现4094个LncRNAs的外显子数量较少(2.4vs.10.2)，转录本长度较长(1903.0 bps.1686.9 bp)。其中，3586个(87.6%)的lncRNAs位于基因间隔区，619个lncRNAs在感染H5N1病毒的鸭体内与对照个体存在差异表达。58个LncRNAs被分成两个与抗甲型流感病毒免疫应答相关的共表达模块。此外，我们还证实了8个lncRNA在感染H5N1病毒后在体内(鸭个体)和体外(鸭胚胎成纤维细胞，DEF细胞)都显示了显著的差异表达，这表明它们可能在甲型流感病毒感染的应答中发挥了重要作用。结论本研究为利用转录组数据在新物种的模式物种中注释lncRNA提供了一个范例。这些数据和分析为研究鸭IncRNAs在甲型流感病毒免疫应答中的作用提供了信息。
BackgroundLong non-coding RNAs (lncRNAs) are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes. For example, human(Homo sapiens)(96,308 vs. 20,376) and mouse(Mus musculus)(87,774 vs. 22,630) have more lncRNA genes than protein-coding genes in the NONCODEv5 database. Recently, mammalian lncRNAs were reported to play critical roles in immune response to influenza A virus infections. Such observation inspired us to identify lncRNAs related to immune response to influenza A virus in duck, which is the most important natural host of influenza A viruses.ResultsWe explored features of 62,447 lncRNAs from human, mouse, chicken, zebrafish and elegans, and developed a pipeline to identify lncRNAs using the identified features with transcriptomic data. We then collected 151,970 assembled transcripts from RNA-Seq data of 21 individuals from three tissues and annotated 4094 duck lncRNAs. Comparing to duck protein-coding transcripts, we found that 4094 lncRNAs had smaller number of exons (2.4vs.10.2) and longer length of transcripts (1903.0 bpvs.1686.9 bp) on average. Among them, 3586 (87.6%) lncRNAs located in intergenic regions and 619 lncRNAs showed differential expression in ducks infected by H5N1 virus when compared to control individuals. 58 lncRNAs were involved into two co-expressional modules related to anti-influenza A virus immune response. Moreover, we confirmed that eight lncRNAs showed remarkably differential expression both in vivo (duck individuals) and in vitro (duck embryo fibroblast cells, DEF cells) after infected with H5N1 viruses, implying they might play important roles in response to influenza A virus infection.ConclusionsThis study presented an example to annotate lncRNA in new species based on model species using transcriptome data. These data and analysis provide information for duck lncRNAs’ function in immune response to influenza A virus.