1. Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing
- Author
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Yutaka Suzuki, Hiroyasu Esumi, Takako Arauchi, Katsuya Tsuchihara, Akinori Kanai, Kousuke Tanimoto, and Sumio Sugano
- Subjects
Genetics ,Promoter ,Biology ,Genome ,Chromatin ,Cell biology ,Transcriptome ,Histone ,biology.protein ,Genetics(clinical) ,Binding site ,Gene ,Genetics (clinical) ,ChIA-PET ,Research Article - Abstract
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.The online version of this article (doi:10.1007/s11568-011-9150-9) contains supplementary material, which is available to authorized users.
- Published
- 2010