Modeling the dynamics of transcriptional gene regulatory networks for animal development

Smadar Ben-Tabou de-Leon, Eric H. Davidson

Research output: Contribution to journalReview articlepeer-review


The dynamic process of cell fate specification is regulated by networks of regulatory genes. The architecture of the network defines the temporal order of specification events. To understand the dynamic control of the developmental process, the kinetics of mRNA and protein synthesis and the response of the cis-regulatory modules to transcription factor concentration must be considered. Here we review mathematical models for mRNA and protein synthesis kinetics which are based on experimental measurements of the rates of the relevant processes. The model comprises the response functions of cis-regulatory modules to their transcription factor inputs, by incorporating binding site occupancy and its dependence on biologically measurable quantities. We use this model to simulate gene expression, to distinguish between cis-regulatory execution of "AND" and "OR" logic functions, rationalize the oscillatory behavior of certain transcriptional auto-repressors and to show how linked subcircuits can be dealt with. Model simulations display the effects of mutation of binding sites, or perturbation of upstream gene expression. The model is a generally useful tool for understanding gene regulation and the dynamics of cell fate specification.

Original languageEnglish
Pages (from-to)317-328
Number of pages12
JournalDevelopmental Biology
Issue number2
StatePublished - 15 Jan 2009
Externally publishedYes

Bibliographical note

Funding Information:
The authors thank Jongmin Nam and Joel Smith for critical review of the manuscript and very insightful comments. Research was supported by NIH grant GM61005. Smadar Ben-Tabou de-Leon was supported by the Human Frontiers Science Program Organization.


  • Dynamics
  • Gene regulation in development
  • Logic functions
  • Mathematical modeling

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology
  • Developmental Biology


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