Tsuchihara Katsuya, Suzuki Yutaka, Wakaguri Hiroyuki, Irie Takuma, Tanimoto Kousuke, Hashimoto Shin-ichi, Matsushima Kouji, Mizushima-Sugano Junko, Yamashita Riu, Nakai Kenta, Bentley David, Esumi Hiroyasu, Sugano Sumio
Cancer Physiology Project, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan.
Nucleic Acids Res. 2009 Apr;37(7):2249-63. doi: 10.1093/nar/gkp066. Epub 2009 Feb 22.
Combining our full-length cDNA method and the massively parallel sequencing technology, we developed a simple method to collect precise positional information of transcriptional start sites (TSSs) together with digital information of the gene-expression levels in a high throughput manner. We applied this method to observe gene-expression changes in a colon cancer cell line cultured in normoxic and hypoxic conditions. We generated more than 100 million 36-base TSS-tag sequences and revealed comprehensive features of hypoxia responsive alterations in the transcriptional landscape of the human genome. The features include presence of inducible 'hot regions' in 54 genomic regions, 220 novel hypoxia inducible promoters that may drive non-protein-coding transcripts, 191 hypoxia responsive alternative promoters and detailed views of 120 novel as well as known hypoxia responsive genes. We further analyzed hypoxic response of different cells using additional 60 million TSS-tags and found that the degree of the gene-expression changes were different among cell lines, possibly reflecting cellular robustness against hypoxia. The novel dynamic figure of the human gene transcriptome will deepen our understanding of the transcriptional program of the human genome as well as bringing new insights into the biology of cancer cells in hypoxia.
结合我们的全长cDNA方法和大规模平行测序技术，我们开发了一种简单的方法，能够以高通量方式收集转录起始位点（TSS）的精确位置信息以及基因表达水平的数字信息。我们将此方法应用于观察在常氧和低氧条件下培养的结肠癌细胞系中的基因表达变化。我们生成了超过1亿条36碱基的TSS标签序列，并揭示了人类基因组转录图谱中缺氧反应性改变的全面特征。这些特征包括54个基因组区域中存在可诱导的“热点区域”、220个可能驱动非蛋白质编码转录本的新型缺氧诱导启动子、191个缺氧反应性可变启动子以及120个新型和已知缺氧反应性基因的详细情况。我们使用另外6000万个TSS标签进一步分析了不同细胞的缺氧反应，发现细胞系之间基因表达变化的程度不同，这可能反映了细胞对缺氧的耐受性。人类基因转录组的这种新型动态图谱将加深我们对人类基因组转录程序的理解，并为缺氧条件下癌细胞的生物学特性带来新的见解。
