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Nucleic Acids Research 2005 33(12):3821-3827; doi:10.1093/nar/gki700
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Published online 13 July 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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{at}oupjournals.org

Article

A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance

Yoshiro Fukue, Noriyuki Sumida, Jun-ichi Tanase and Takashi Ohyama*

Department of Biology, Faculty of Science and Engineering, Konan University 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan

*To whom correspondence should be addressed. Tel: +81 78 435 2547; Fax: +81 78 435 2539; Email: ohyama{at}konan-u.ac.jp

Received May 11, 2005. Revised June 22, 2005. Accepted June 22, 2005.

A recent study revealed that TATA boxes and initiator sequences have a common anomalous mechanical property, i.e. they comprise distinctive flexible and rigid sequences when compared with the other parts of the promoter region. In the present study, using the flexibility parameters from two different models, we calculated the average flexibility profiles of 1004 human promoters that do not contain canonical promoter elements, such as a TATA box, initiator (Inr) sequence, downstream promoter element or a GC box, and those of 382 human promoters that contain the GC box only. Here, we show that they have a common characteristic mechanical property that is strikingly similar to those of the TATA box-containing or Inr-containing promoters. Their most interesting feature is that the TATA- or Inr-corresponding region lies in the several nucleotides around the transcription start site. We have also found that a dinucleotide step from –1 to +1 (transcription start site) has a slight tendency to adopt CA that is known to be flexible. We also demonstrate that certain synthetic DNA fragments designed to mimic the average mechanical property of these 1386 promoters can drive transcription. This distinctive mechanical property may be the hallmark of a promoter.


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