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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Additional file 14 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736747
Additional file 4 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736717
Additional file 9 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736732
Additional file 7 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736726
Additional file 8 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736729
Additional file 10 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736735
Additional file 6 of Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736723

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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