Global analysis of in vivo EGR1‐binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencing
Global analysis of in vivo EGR1‐binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencing
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DOI：
10.1002/elps.201000094
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发表时间：
2010-09
期刊：
影响因子：
2.9
通讯作者：
Chao Tang;Xiaolong Shi;Wei Wang;Dequan Zhou;Jing Tu;Xueying Xie;Qinyu Ge;P. Xiao;Xiao Sun;Zuhong Lu
中科院分区：
文献类型：
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作者：
Chao Tang;Xiaolong Shi;Wei Wang;Dequan Zhou;Jing Tu;Xueying Xie;Qinyu Ge;P. Xiao;Xiao Sun;Zuhong Lu
早期生长反应基因1（EGR1）与佛波酯诱导的巨核细胞分化有关。但EGFR 1在此过程中的分子机制尚未得到广泛研究。在全球范围内鉴定直接EGR1靶基因对于我们理解EGR1如何促进这一过程至关重要。在这项研究中，我们提供了一个全球性的调查结合的K562细胞中的EGFR 1的染色质免疫沉淀和大规模平行测序的位置。在佛波醇12-肉豆蔻酸酯13-乙酸酯处理的K562细胞中鉴定了超过14000个高度可信的体内EGFR 1结合位点。这些与EGR1结合相关的基因组位点中有70%以上位于注释基因区域周围。6138个推定的EGR1靶基因的分子功能分类显示，转录因子类（695 6138; 11%）是最大的显着富集的一个。结果表明，该方法获得了较高的基因组覆盖率和阳性检出率。对EGR1靶基因的全基因组研究有助于更好地了解EGR1调控的基因及其下游通路在巨核细胞分化中的作用。
Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by phorbol ester. But the molecule mechanism of EGR1 in this process has not been widely investigated. The identification of direct EGR1 target genes in a global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cells using chromatin immunoprecipitation and massively parallel sequencing. Over 14 000 highly confident in vivo EGR1 binding sites were identified in phorbol 12‐myristate 13‐acetate‐treated K562 cells. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. Molecular functional classification of 6138 putative EGR1 target genes showed that the transcription factor class (695 of 6138; 11%) is the largest significantly enriched one. The results showed that a high coverage of the genome and a high positive rate achieve were achieved. This whole genome study on the EGR1 targets may provide a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation.