Deep sequencing of the zebrafish transcriptome response to mycobacterium infection
Deep sequencing of the zebrafish transcriptome response to mycobacterium infection
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DOI：
10.1016/j.molimm.2009.07.002
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发表时间：
2009-09-01
影响因子：
3.6
通讯作者：
Meijer, Annemarie H.
中科院分区：
文献类型：
--
作者：
Hegedus, Zoltan;Zakrzewska, Anna;Meijer, Annemarie H.
新型高通量深度测序技术极大地改变了研究转录组功能复杂性的方式。在此，我们首次报道利用该技术深入了解与传染病过程相关的广泛转录反应。我们使用Solexa/Illumina的数字基因表达（DGE）系统（一种基于标签的转录组测序方法），研究了脊椎动物模型斑马鱼中分枝杆菌诱导的转录组变化。我们每个样本获得了超过500万个标签的测序深度，且重复样本之间具有很强的相关性。标签定位表明，健康和受感染的成年斑马鱼表达转录数据库中所有基因的70%以上。将这些数据与之前的多平台微阵列分析进行比较，结果显示两种技术都能识别出相似功能基因组的调控。然而，DGE分析的无偏性提供了微阵列分析无法实现的见解。特别是，我们表明DGE数据集有助于验证预测的基因模型，并使我们能够检测到分枝杆菌调控的不同转录异构体之间的转换。此外，感染诱导的DGE标签的基因组定位揭示了一些新的转录形式，之前基于EST的表达证据中缺乏这些转录形式。总之，我们的深度测序分析深入揭示了宿主对分枝杆菌感染反应的高度转录复杂性，并导致了在感染个体中诱导表达的新基因产物的发现和验证。（C）2009 Elsevier Ltd.保留所有权利。
Novel high-throughput deep sequencing technology has dramatically changed the way that the functional complexity of transcriptomes can be studied. Here we report on the first use of this technology to gain insight into the wide range of transcriptional responses that are associated with an infectious disease process. Using Solexa/Illumina's digital gene expression (DGE) system, a tag-based transcriptome sequencing method, we investigated mycobacterium-induced transcriptome changes in a model vertebrate species, the zebrafish. We obtained a sequencing depth of over 5 million tags per sample with strong correlation between replicates. Tag mapping indicated that healthy and infected adult zebrafish express over 70% of all genes represented in transcript databases. Comparison of the data with a previous multi-platform microarray analysis showed that both types of technologies identified regulation of similar functional groups of genes. However, the unbiased nature of DGE analysis provided insights that microarray analysis could not have achieved. In particular, we show that DGE data sets are instrumental for verification of predicted gene models and allowed us to detect mycobacterium-regulated switching between different transcript isoforms. Moreover, genomic mapping of infection-induced DGE tags revealed novel transcript forms for which any previous EST-based evidence of expression was lacking. In conclusion, our deep sequencing analysis revealed in depth the high degree of transcriptional complexity of the host response to mycobacterial infection and resulted in the discovery and validation of new gene products with induced expression in infected individuals. (C) 2009 Elsevier Ltd. All rights reserved.