5′-end SAGE for the analysis of transcriptional start sites (original) (raw)

Nature Biotechnology volume 22, pages 1146–1149 (2004)Cite this article

Abstract

Identification of the mRNA start site is essential in establishing the full-length cDNA sequence of a gene and analyzing its promoter region, which regulates gene expression. Here we describe the development of a 5′-end serial analysis of gene expression (5′ SAGE) that can be used to globally identify transcriptional start sites and the frequency of individual mRNAs. Of the 25,684 5′ SAGE tags in the HEK293 human cell library, 19,893 matched to the human genome. Among 15,448 tags in one locus of the genome, 85.8%–96.1% of the 5′ SAGE tags were assigned within −500 to +200 nt of mRNA start sites using the RefSeq, UniGene and DBTSS databases. This technique should facilitate 5′-end transcriptome analysis in a variety of cells and tissues.

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Acknowledgements

This work was supported by Grant-in-Aid for Scientific Research on Priority Areas (C) “Medical Genome Science” from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

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Author notes

  1. Yutaka Suzuki and Yasuhiro Kasai: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Preventive Medicine, School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
    Shin-ichi Hashimoto, Kei Morohoshi & Kouji Matsushima
  2. Department of Virology, Institute of Medical Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
    Yutaka Suzuki & Sumio Sugano
  3. Department of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
    Yasuhiro Kasai, Tomoyuki Yamada, Jun Sese & Shinichi Morishita

Authors

  1. Shin-ichi Hashimoto
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  2. Yutaka Suzuki
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  3. Yasuhiro Kasai
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  4. Kei Morohoshi
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  5. Tomoyuki Yamada
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  6. Jun Sese
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  7. Shinichi Morishita
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  8. Sumio Sugano
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  9. Kouji Matsushima
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Corresponding author

Correspondence toKouji Matsushima.

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Hashimoto, Si., Suzuki, Y., Kasai, Y. et al. 5′-end SAGE for the analysis of transcriptional start sites.Nat Biotechnol 22, 1146–1149 (2004). https://doi.org/10.1038/nbt998

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