Skip Navigation

Nucleic Acids Research 2004 32(19):5834-5840; doi:10.1093/nar/gkh905
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (335K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (10)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Fukue, Y.
Right arrow Articles by Ohyama, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fukue, Y.
Right arrow Articles by Ohyama, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 1 November 2004

Nucleic Acids Research, Vol. 32 No. 19 © Oxford University Press 2004; all rights reserved

Core promoter elements of eukaryotic genes have a highly distinctive mechanical property

Yoshiro Fukue, Noriyuki Sumida, Jun-ichi Nishikawa 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 August 24, 2004; Revised and Accepted October 6, 2004

In spite of the abundant data on DNA sequence, the mechanical aspects of promoter DNA remain poorly understood. We classified 1871 human and 196 mouse RNA polymerase II promoters and investigated average flexibility profiles of the human promoters containing either a TATA box or an initiator (Inr) sequence only. Here, we show that TATA boxes and Inr sequences have a common anomalous mechanical property: they are comprised of distinctively flexible and rigid sequences, compared with the other parts of the promoter region. The +2 position in the Inr consensus sequence does not favor adenine to keep the high flexibility and thus this position is more accurately represented as ‘T, G, C>>A’. Additionally, it was also found that DNA region upstream of TATA box or Inr sequence is more rigid than region downstream of each element. These properties may function as a marker for recognition by TATA-binding protein and Inr-binding protein.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Physiol. GenomicsHome page
V. L. M. Herrera, P. Bagamasbad, T. Didishvili, J. L. Decano, and N. Ruiz-Opazo
Overlapping genes in Nalp6/PYPAF5 locus encode two V2-type vasopressin isoreceptors: angiotensin-vasopressin receptor (AVR) and non-AVR
Physiol Genomics, June 1, 2008; 34(1): 65 - 77.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
T. Abeel, Y. Saeys, E. Bonnet, P. Rouze, and Y. Van de Peer
Generic eukaryotic core promoter prediction using structural features of DNA
Genome Res., February 1, 2008; 18(2): 310 - 323.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Florquin, Y. Saeys, S. Degroeve, P. Rouze, and Y. Van de Peer
Large-scale structural analysis of the core promoter in mammalian and plant genomes
Nucleic Acids Res., July 27, 2005; 33(13): 4255 - 4264.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Fukue, N. Sumida, J.-i. Tanase, and T. Ohyama
A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance
Nucleic Acids Res., July 13, 2005; 33(12): 3821 - 3827.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.