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DNA Research Advance Access published online on May 23, 2007
DNA Research, doi:10.1093/dnares/dsm006
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© The Author 2007. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome

Yuta Sakakibara1,3, Takuma Irie1, Yutaka Suzuki1,*, Riu Yamashita2, Hiroyuki Wakaguri1, Akinori Kanai1, Joe Chiba3, Toshihisa Takagi1, Junko Mizushima-Sugano1,4, Shin-ichi Hashimoto5, Kenta Nakai2 and Sumio Sugano1

1 Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
2 Human Genome Center, The Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
3 Faculty of Industrial Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
4 Laboratory of Viral Infection II, Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Sirokane Minato-ku, Tokyo 108-8641, Japan
5 School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyoku, Tokyo 113-0033, Japan

Received 14 December 2006 ; revised 15 March 2007

In order to understand an overview of promoter activities intrinsic to primary DNA sequences in the human genome within a particular cell type, we carried out systematic quantitative luciferase assays of DNA fragments corresponding to putative promoters for 472 human genes which are expressed in HEK (human embryonic kidney epithelial) 293 cells. We observed the promoter activities of them were distributed in a bimodal manner; putative promoters belonging to the first group (with strong promoter activities) were designated as P1 and the latter (with weak promoter activities) as P2. The frequencies of the TATA-boxes, the CpG islands, and the overall G + C-contents were significantly different between these two populations, indicating there are two separate groups of promoters. Interestingly, similar analysis using 251 randomly isolated genomic DNA fragments showed that P2-type promoter occasionally occurs within the human genome. Furthermore, 35 DNA fragments corresponding to putative promoters of non-protein-coding transcripts (ncRNAs) shared similar features with the P2 in both promoter activities and sequence compositions. At least, a part of ncRNAs, which have been massively identified by full-length cDNA projects with no functional relevance inferred, may have originated from those sporadic promoter activities of primary DNA sequences inherent to the human genome.

Key words: human genome; promoter; transcriptional start site

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

Communicated by Minoru Ko


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