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Nucleic Acids Research Advance Access originally published online on February 22, 2009
Nucleic Acids Research 2009 37(7):2249-2263; doi:10.1093/nar/gkp066
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Nucleic Acids Research, 2009, Vol. 37, No. 7 2249-2263
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Massive transcriptional start site analysis of human genes in hypoxia cells

Katsuya Tsuchihara1, Yutaka Suzuki2,*, Hiroyuki Wakaguri2, Takuma Irie2, Kousuke Tanimoto2, Shin-ichi Hashimoto3, Kouji Matsushima3, Junko Mizushima-Sugano2,4, Riu Yamashita5, Kenta Nakai5, David Bentley6, Hiroyasu Esumi1 and Sumio Sugano2

1Cancer Physiology Project, Research Center for Innovative Oncology, National Cancer Center Hospital East: 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, 2Graduate School of Frontier Sciences, the University of Tokyo: 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, 3Graduate School of Medicine, the University of Tokyo: 7-3-1 Hongo, Bunkyokyu, Tokyo 113-0033, 4Laboratory of Molecular Virology, Kitasato Institute for Life Sciences, Kitasato University: 5-9-1 Shirokane, Minatoku, Tokyo 108-8641, 5Institute of Medical Science, the University of Tokyo: 4-6-1 Shirokenedai, Minatoku, Tokyo 108-8639, Japan and 6Illumina, Inc: 25861 Industrial Boulevard Hayward, CA 94545, USA

*To whom correspondence should be addressed. Tel/Fax: +81 4 7136 3607; Email: ysuzuki{at}k.u-tokyo.ac.jp

Received October 3, 2008. Revised January 20, 2009. Accepted January 22, 2009.

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.


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R. Yamashita, H. Wakaguri, S. Sugano, Y. Suzuki, and K. Nakai
DBTSS provides a tissue specific dynamic view of Transcription Start Sites
Nucleic Acids Res., November 12, 2009; (2009) gkp1017v1.
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