A Comprehensive Profile of ChIP-Seq-Based STAT1 Target Genes Suggests the Complexity of STAT1-Mediated Gene Regulatory Mechanisms.
A Comprehensive Profile of ChIP-Seq-Based STAT1 Target Genes Suggests the Complexity of STAT1-Mediated Gene Regulatory Mechanisms.
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DOI：
10.4137/grsb.s11433
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
Tabunoki H
中科院分区：
文献类型：
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作者：
Satoh J;Tabunoki H
干扰素-γ（IFNγ）在巨噬细胞活化、T辅助细胞和调节细胞分化、防御细胞内病原体、组织重塑和肿瘤监视中起关键作用。IFNγ的多种生物学功能是通过直接激活信号转导和转录激活因子1（STAT 1）以及众多下游效应基因来介导的。由于STAT 1靶基因网络的扰动与自身免疫性疾病和癌症的发展密切相关，因此表征这些网络的全局图像非常重要。染色质免疫沉淀后进行深度测序（ChIP-Seq）提供了一种高效的DNA结合蛋白全基因组分析方法。我们分析了来自ENCODE项目的IFNγ刺激的HeLa S3细胞的STAT 1 ChIP-Seq数据集，沿着微阵列上的转录组分析。我们鉴定了1，441个蛋白质编码基因的严格ChIP-Seq峰。它们位于启动子区（21.5%），更多位于内含子区（72.2%），并存在IFNγ激活位点（GAS）元件。在1，441个STAT 1靶基因中，212个基因是已知的IFN调节基因（IRGs），194个基因（13.5%）通过转录组分析实际上在响应IFNγ时上调。上调的基因组构成了宿主防御感染的关键IFN信号分子网络，其中干扰素调节因子（IRF）和STAT转录因子作为生物学上重要的分子连接集中的枢纽。在内含子区域具有峰值位置的基因在IFNγ应答中显示出显著较低的表达水平。这些结果表明，STAT 1与GAS的结合不足以完全激活靶基因，表明STAT 1介导的基因调控机制的高度复杂性。
Interferon-gamma (IFNγ) plays a key role in macrophage activation, T helper and regulatory cell differentiation, defense against intracellular pathogens, tissue remodeling, and tumor surveillance. The diverse biological functions of IFNγ are mediated by direct activation of signal transducer and activator of transcription 1 (STAT1) as well as numerous downstream effector genes. Because a perturbation in STAT1 target gene networks is closely associated with development of autoimmune diseases and cancers, it is important to characterize the global picture of these networks. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) provides a highly efficient method for genome-wide profiling of DNA-binding proteins. We analyzed the STAT1 ChIP-Seq dataset of IFNγ-stimulated HeLa S3 cells derived from the ENCODE project, along with transcriptome analysis on microarray. We identified 1,441 stringent ChIP-Seq peaks of protein-coding genes. They were located in the promoter (21.5%) and more often in intronic regions (72.2%) with an existence of IFNγ-activated site (GAS) elements. Among the 1,441 STAT1 target genes, 212 genes are known IFN-regulated genes (IRGs) and 194 genes (13.5%) are actually upregulated in response to IFNγ by transcriptome analysis. The panel of upregulated genes constituted IFN-signaling molecular networks pivotal for host defense against infections, where interferon-regulatory factor (IRF) and STAT transcription factors serve as a hub on which biologically important molecular connections concentrate. The genes with the peak location in intronic regions showed significantly lower expression levels in response to IFNγ. These results indicate that the binding of STAT1 to GAS is not sufficient to fully activate target genes, suggesting the high complexity of STAT1-mediated gene regulatory mechanisms.