2012 Fiscal Year Final Research Report
Integrated transcriptome analysis of cancer cells in response to hypoxic shock using next generation sequencer
| Project/Area Number |
22681027
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| Research Category |
Grant-in-Aid for Young Scientists (A)
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| Allocation Type | Single-year Grants |
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| Research Field |
Genome biology
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| Research Institution | The University of Tokyo |
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Principal Investigator |
SUZUKI Yutaka 東京大学, 大学院・新領域創成科学研究科, 准教授 (40323646)
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| Project Period (FY) |
2010 – 2012
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| Keywords | 次世代シークエンサー / 低酸素応答 / トランスクリプトーム / 転写開始転 クロマチン / Chip Seq 解析 |
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| Research Abstract |
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.
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