Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing
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- 作者：Kousuke Tanimoto (1)
Katsuya Tsuchihara (2)
Akinori Kanai (1)
Takako Arauchi (1)
Hiroyasu Esumi (2)
Yutaka Suzuki (1)
Sumio Sugano (1) - 关键词：HIF ; 1 alpha ; Hypoxia ; ChIP ; Seq ; Transcriptome
- 刊名：The HUGO Journal
- 出版年：2010
- 出版时间：December 2010
- 年：2010
- 卷：4
- 期：1-4
- 页码：35-48
- 全文大小：708KB
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Katsuya Tsuchihara (2)
Akinori Kanai (1)
Takako Arauchi (1)
Hiroyasu Esumi (2)
Yutaka Suzuki (1)
Sumio Sugano (1)
1. Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
2. Cancer Physiology Project, Research Center for Innovative Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan - ISSN：1877-6566
文摘
We identified 531 and 616 putative HIF-1α target sites by ChIP-Seq in the cancerous cell line DLD-1 and the non-cancerous cell line TIG-3, respectively. We also examined the positions and expression levels of transcriptional start sites (TSSs) in these cell lines using our TSS-Seq method. We observed that 121 and 48 genes in DLD-1 and TIG-3 cells, respectively, had HIF-1α binding sites in proximal regions of the previously reported TSSs that were up-regulated at the transcriptional level. In addition, 193 and 123 of the HIF-1α target sites, respectively, were located in proximal regions of previously uncharacterized TSSs, namely, TSSs of putative alternative promoters of protein-coding genes or promoters of putative non-protein-coding transcripts. The hypoxic response of DLD-1 cells was more significant than that of TIG-3 cells with respect to both the number of target sites and the degree of induced changes in transcript expression. The Nucleosome-Seq and ChIP-Seq analyses of histone modifications revealed that the chromatin formed an open structure in regions surrounding the HIF-1α binding sites, but this event occurred prior to the actual binding of HIF-1α. Different cellular histories may be encoded by chromatin structures and determine the activation of specific genes in response to hypoxic shock.