Skip Navigation


Journal of Biochemistry Advance Access originally published online on July 25, 2007
Journal of Biochemistry 2007 142(2):135-144; doi:10.1093/jb/mvm151
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplementary data
Right arrow All Versions of this Article:
142/2/135    most recent
mvm151v1
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 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 Request Permissions
Google Scholar
Right arrow Articles by Yang, H.-T.
Right arrow Articles by Hwang, M.-J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yang, H.-T.
Right arrow Articles by Hwang, M.-J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Japanese Biochemical Society.

An Analytical Rate Expression for the Kinetics of Gene Transcription Mediated by Dimeric Transcription Factors

Hsih-Te Yang1,3, Chao-Ping Hsu2 and Ming-Jing Hwang3,*

1Institute of Biochemistry and Molecular Biology, National Yang-Ming University; 2Institute of Chemistry and 3Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan

*To whom correspondence should be addressed. Tel: +886-2-2789-9033, Fax: +886-2-2788-7641, E-mail: mjhwang{at}ibms.sinica.edu.tw

Received April 17, 2007; Accepted June 1, 2007


  Abstract

To model gene transcription kinetics, empirical fitting with the Hill function or S-system is often used. In this study, we derived an analytical expression for gene transcription rates in a manner similar to that developed for enzyme kinetics to describe the kinetics of gene transcription mediated by dimeric transcription factors (TFs) such as Gcn4p, a Saccharomyces cerevisiae master gene regulator. We showed that the analytical rate expression and its parameters estimated from several sets of experimental data could accurately reproduce the experimentally measured promoter-binding activity of Gcn4p. Furthermore, the analytical rate expression allowed us to derive analytically, rather than fit empirically, the parameters of the Hill function and S-system for use in modelling transcription kinetics. We found that a plot of gene transcription rate against Gcn4p concentration gave a sigmoidal dose-response curve with a positive co-operativity Hill coefficient (~1.25), in accordance with previous experimental findings on the promoter binding of dimeric TFs. The characteristics of the dose-response curve around the estimated cellular Gcn4p concentration suggest that transcription regulation is efficiently controlled under physiological conditions. This work is a useful initial step towards analytically modelling and simulating complicated gene transcription networks.

Key Words: enzyme kinetics, gene transcription modelling, Hill function, S-system, transcription kinetics

Abbreviations: MM, Michaelis–Menten; PIC, pre-initiation complex; TF, transcription factor


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
 BioinformaticsHome page
E. Cinquemani, A. Milias-Argeitis, S. Summers, and J. Lygeros
Stochastic dynamics of genetic networks: modelling and parameter identification
Bioinformatics, December 1, 2008; 24(23): 2748 - 2754.
[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.