Skip Navigation


Bioinformatics Advance Access originally published online on November 30, 2004
Bioinformatics 2005 21(8):1295-1300; doi:10.1093/bioinformatics/bti172
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/8/1295    most recent
bti172v1
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 (23)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Gershenzon, N. I.
Right arrow Articles by Ioshikhes, I. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gershenzon, N. I.
Right arrow Articles by Ioshikhes, I. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Synergy of human Pol II core promoter elements revealed by statistical sequence analysis

Naum I. Gershenzon and Ilya P. Ioshikhes *

Department of Biomedical Informatics, The Ohio State University 3184 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA

*To whom correspondence should be addressed.

Motivation: The subject of our paper is bioinformatics analysis of the distinguishing features of human promoter DNA sequences, in particular of synergetic combinations of core promoter elements therein. We suppose that specific scenarios of transcription initiation are essentially related to various particular implementations of the interaction of basal transcription machinery with promoter DNA, depending on the presence and mutual positioning of core promoter elements.

Results: In addition to the combinations of core promoter elements previously experimentally confirmed [TATA box and Initiator (Inr), Downstream Promoter Element (DPE) and Inr, and TFIIB recognition element (BRE) and TATA box] we propose other alternate synergetic combinations: BRE and Inr, BRE and DPE, and TATA and DPE with respective models. The suggestion is based on a high statistical significance of the alternate combinations in promoters, comparable with the significance of the known combinations. We also present arguments that the BRE element is statistically more important than previously thought, and suggest possible mechanisms of action of the core elements in the promoters with multiple transcription start sites.

Contact: ioschikhes-1{at}medctr.osu.edu

Supplementary information: Supplementary information is available at http://bmi.osu.edu/~ilya/synergy/Gershenzon_SuppMat-R.pdf


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
 Biophys. JHome page
C. H. Choi, Z. Rapti, V. Gelev, M. R. Hacker, B. Alexandrov, E. J. Park, J. S. Park, N. Horikoshi, A. Smerzi, K. O. Rasmussen, et al.
Profiling the Thermodynamic Softness of Adenoviral Promoters
Biophys. J., July 15, 2008; 95(2): 597 - 608.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. C. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, and A. Sandelin
A code for transcription initiation in mammalian genomes
Genome Res., January 1, 2008; 18(1): 1 - 12.
[Abstract] [Full Text] [PDF]

Home page
 Genes Dev.Home page
Y. Isogai, S. Keles, M. Prestel, A. Hochheimer, and R. Tjian
Transcription of histone gene cluster by differential core-promoter factors
Genes & Dev., November 15, 2007; 21(22): 2936 - 2949.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
B. Malecova, P. Gross, M. Boyer-Guittaut, S. Yavuz, and T. Oelgeschlager
The Initiator Core Promoter Element Antagonizes Repression of TATA-directed Transcription by Negative Cofactor NC2
J. Biol. Chem., August 24, 2007; 282(34): 24767 - 24776.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Vardhanabhuti, J. Wang, and S. Hannenhalli
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
Nucleic Acids Res., May 11, 2007; 35(10): 3203 - 3213.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. J. Stewart, J. A. Fischbeck, X. Chen, and L. A. Stargell
Non-optimal TATA Elements Exhibit Diverse Mechanistic Consequences
J. Biol. Chem., August 11, 2006; 281(32): 22665 - 22673.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
D.-H. Lee, N. Gershenzon, M. Gupta, I. P. Ioshikhes, D. Reinberg, and B. A. Lewis
Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1
Mol. Cell. Biol., November 1, 2005; 25(21): 9674 - 9686.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. I. Gershenzon, G. D. Stormo, and I. P. Ioshikhes
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites
Nucleic Acids Res., April 22, 2005; 33(7): 2290 - 2301.
[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.