Cited by 109Gene Regulatory Network AnalysisDevelopmental Biology and Gene RegulationGenomics and Chromatin Dynamics

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Modeling the dynamics of transcriptional gene regulatory networks for animal development

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Ben-Tabou de-Leon, Smadar, Davidson, Eric H.·2009·Developmental Biology

DOI 10.1016/j.ydbio.2008.10.043PMC PMC4100934

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Abstract

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.

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Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566
On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development
Peshkin, L., Wühr, M., Pearl, E. J., Haas, W., Freeman, R. M., Gerhart, J. C., Klein, A. M., Horb, M. E., Gygi, S. P., & Kirschner, M. W. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.10.010 · Cited by 219
Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
Zhong, M., Niu, W., Lu, Z. J., Sarov, M., Murray, J. I., Janette, J., Raha, D., Sheaffer, K. L., Lam, H. Y. K., Preston, E. A., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000848 · Cited by 170
How subtle changes in 3D structure can create large changes in transcription
Xiao, J. Y., Hafner, A., & Boettiger, A. N. (2021) · eLife · doi:10.7554/elife.64320 · Cited by 162
Systematic analysis of posttranscriptional gene expression
Morris, A. R., Mukherjee, N., & Keene, J. D. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.54 · Cited by 112

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Authors: Ben-Tabou de-Leon, S., & Davidson, E. H.
Affiliations: California Institute of Technology (US)
Corresponding author: Davidson, Eric H.
Venue: Developmental Biology
Publisher: Elsevier BV
Published: 2009-01
Volume: 325
Issue: 2
Pages: 317-328
ISSN: 0012-1606 (ISSN-L)
DOI: 10.1016/j.ydbio.2008.10.043
PMC: PMC4100934
OpenAlex: W2120009112
Cited by: 99
References: 106
Citations by year: 2025: 1 · 2024: 8 · 2023: 3 · 2022: 3 · 2021: 5 · 2020: 5 · 2019: 5 · 2018: 4 · 2017: 9 · 2016: 6 · 2015: 10 · 2014: 3 · 2013: 6 · 2012: 6
FWCI: 0.64
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 1694 d)
doi.org/10.15223/policy-017 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-012 (stm-asf)
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-004 (stm-asf)
Locations: Developmental Biology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
CaltechAUTHORS (California Institute of Technology) (submittedVersion)
Funders: National Institutes of Health
National Institute of General Medical Sciences (GM 61005, R01GM061005)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords: cell fate specification, animal development, protein synthesis kinetics, cis-regulatory modules, response functions, gene expression oscillations, binding site mutations, mathematical modeling of gene regulation
MeSH terms: Animals, Binding Sites, Biological Clocks, DNA-Binding Proteins, Genes, Regulator, Kinetics, Models, Genetic, RNA, Messenger, Transcription Factors, Transcription, Genetic, Protein Biosynthesis, Gene Expression Regulation, Developmental, Gene Regulatory Networks

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Modeling the dynamics of transcriptional gene regulatory networks for animal development

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