Integrated transcriptome analysis of cancer cells in response to hypoxic shock using next generation sequencer

我使用下一代测序仪对结肠癌细胞系DLD-1在低氧休克反应中进行了整合转录组分析。我生成了1亿个TSS标签，并关联了各种表观基因组和转录组信息。也就是说，该数据集包括HIF 1的ChIP Seq数据，HIF 1是响应缺氧休克的关键转录因子，代表性的活性和抑制性组蛋白标记物和RNA聚合酶II。该数据进一步与细胞核、细胞质和多核糖体组分的RNA Seq数据相关。综合分析数据显示，染色质形成开放结构之前，实际缺氧休克。我们还证明了基因表达调控在转录组层的各个水平上发挥作用，如表观基因组调控，转录起始，延伸和最终降解。这是第一份报告阐明了缺氧条件下癌细胞转录组调控的全面观点，因此，应为未来分析癌症如何在体内缺氧环境中生存提供有用的线索。

I conducted integrated transcriptome analysis of a colon cancer cell line, DLD-1, in response to hypoxic shock using next generation sequencer. I generated 100 million TSS tags and associated a wide variety of epigenomic and transcriptomic information. Namely, this dataset include ChIP Seq data of HIF1, which is a pivotal transcription factor in response to hypoxic shock, representative active and repressive histone markers and RNApolymerase II. This data was further associated with RNA Seq data of nucleus, cytoplasm and polysome fractions. Integrative analysis of the data revealed that chromatin forms open structure in prior to actual hypoxic shock. We also demonstrate that gene expression regulations are exerted at various levels of transcriptome layers, such as epigenomic regulations, transcriptional initiation, elongations and finally degradations. This is the first report shed light on comprehensive views on the transcriptome regulations in cancer cells in hypoxic conditions, thus, should give useful clues for the future analysis how cancers survive in hypoxic environments in vivo.