Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection
Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection
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DOI：
10.1016/j.fsi.2010.08.022
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发表时间：
2011-11-01
影响因子：
4.7
通讯作者：
Meijer, Annemarie H.
中科院分区：
文献类型：
--
作者：
Ordas, Anita;Hegedus, Zoltan;Meijer, Annemarie H.
伤寒沙门氏菌(鼠伤寒沙门氏菌)能引起斑马鱼胚胎的致死性炎症感染。为了在转录组水平上表征胚胎的先天宿主反应，我们通过Illumina下一代测序分析扩展并验证了先前的微阵列数据。我们使用基于标签的测序方法(DGE或Tag-Seq)从对照斑马鱼胚胎和感染沙门氏菌的斑马鱼胚胎中获得了1000万个序列读数，使用全转录测序(RNA-Seq)获得了1500万个序列读数，分别与28,716个已知EnSemb1转录本中的约65%和85%相对应。这两种测序方法都显示出每个转录本的序列读取计数和241个差异表达的转录本的重叠。观察到165个转录本与先前的微阵列数据有较低的重叠。基于基于测序和基于微阵列的组合转录组数据，我们编辑了斑马鱼胚胎中感染反应基因的注释参考集，编码转录因子、信号转导蛋白、细胞因子和趋化因子、补体因子、参与细胞凋亡和蛋白分解的蛋白、具有抗微生物活性的蛋白以及许多已知或新的与免疫反应无关的蛋白。此外，通过比较斑马鱼胚胎中鼠伤寒沙门氏菌感染的深层测序数据和成年斑马鱼中海洋分枝杆菌感染的深层测序数据，我们获得了一组共同的感染反应基因。该基因集由已知和推测的天然宿主防御基因组成，这些基因在缺乏和存在完全发育的适应性免疫系统的情况下表达，为未来利用斑马鱼感染模型研究宿主与病原体的相互作用提供了有价值的参考。(C)2010爱思唯尔有限公司。保留所有权利。
Salmonella enterica serovar Typhimurium (S. typhimurium) bacteria cause an inflammatory and lethal infection in zebrafish embryos. To characterize the embryonic innate host response at the transcriptome level, we have extended and validated previous microarray data by Illumina next-generation sequencing analysis. We obtained 10 million sequence reads from control and Salmonella-infected zebrafish embryos using a tag-based sequencing method (DGE or Tag-Seq) and 15 million reads using whole transcript sequencing (RNA-Seq), which respectively mapped to circa 65% and 85% of 28,716 known Ensembl transcripts. Both sequencing methods showed a strong correlation of sequence read counts per transcript and an overlap of 241 transcripts differentially expressed in response to infection. A lower overlap of 165 transcripts was observed with previous microarray data. Based on the combined sequencing-based and microarray-based transcriptome data we compiled an annotated reference set of infection-responsive genes in zebrafish embryos, encoding transcription factors, signal transduction proteins, cytokines and chemokines, complement factors, proteins involved in apoptosis and proteolysis, proteins with antimicrobial activities, as well as many known or novel proteins not previously linked to the immune response. Furthermore, by comparison of the deep sequencing data of S. typhimurium infection in zebrafish embryos with previous deep sequencing data of Mycobacterium marinum infection in adult zebrafish we derived a common set of infection-responsive genes. This gene set consists of known and putative innate host defense genes that are expressed both in the absence and presence of a fully developed adaptive immune system and that provide a valuable reference for future studies of host-pathogen interactions using zebrafish infection models. (C) 2010 Elsevier Ltd. All rights reserved.