Stochastic modeling of gene activation and applications to cell regulation

DOI10.1016/J.JTBI.2010.11.032MaRDI QIDQ1670565zbMATH OpenOpenAlexWikidataFDO

Authors G. Malherbe, D. Holcman

Publication date 6 September 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1010.3001

zbMATH Keywords

cell differentiationmorphogenetic gradientgene activationgenetic switchstochastic binding

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Ecology (92D40)

Abstract: Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we study the arrival time of several TFs to multiple binding sites and derive, in the presence of competitive binding ligands, the probability that several target sites are bound. We then apply our results to the hunchback regulation by bicoid in the fly embryo and we propose a general mechanism that allows cells to read a morphogenetic gradient and specialize according to their position in the embryo.

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Cited in

(9)

• Polymer physics of nuclear organization and function
• Stochastic modelling of gene regulatory networks
• A Stochastic Model of the Production of Multiple Proteins in Cells
• Modelling Nonstationary Gene Regulatory Processes
• Random dynamics of gene transcription activation in single cells
• Models of transcription factor binding: sensitivity of activation functions to model assumptions
• Transcription factor target site search and gene regulation in a background of unspecific binding sites
• A kinetic mechanism for \textit{Drosophila} bicoid cooperative binding
• A mathematical model for enhancer activation kinetics during cell differentiation

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