Skip to content

Research at St Andrews

Diffusion driven oscillations in gene regulatory networks

Research output: Contribution to journalArticle

Abstract

Gene regulatory networks (GRNs) play an important role in maintaining cellular function by correctly timing key processes such as cell division and apoptosis. GRNs are known to contain similar structural components, which describe how genes and proteins within a network interact - typically by feedback. In many GRNs, proteins bind to gene-sites in the nucleus thereby altering the transcription rate. If the binding reduces the transcription rate there is a negative feedback leading to oscillatory behaviour in mRNA and protein levels, both spatially (e.g. by observing fluorescently labelled molecules in single cells) and temporally (e.g. by observing protein/mRNA levels over time). Mathematical modelling of GRNs has focussed on such oscillatory behaviour. Recent computational modelling has demonstrated that spatial movement of the molecules is a vital component of GRNs, while it has been proved rigorously that the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf-bifurcation. In this paper we consider the spatial aspect further by considering the specific location of gene and protein production, showing that there is an optimum range for the distance between an mRNA gene-site and a protein production site in order to achieve oscillations. We first present a model of a well-known GRN, the Hes1 system, and then extend the approach to examine spatio-temporal models of synthetic GRNs e.g. n-gene repressilator and activator-repressor systems. By incorporating the idea of production sites into such models we show that the spatial component is vital to fully understand GRN dynamics.
Close

Details

Original languageEnglish
Pages (from-to)51-70
Number of pages20
JournalJournal of Theoretical Biology
Volume407
Early online date20 Jul 2016
DOIs
Publication statusPublished - 21 Oct 2016

    Research areas

  • Hes1 protein, Synthetic networks, Repressilators, Activator-repressor systems, Spatial modelling

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

Related by journal

  1. A theory for investment across defences triggered at different stages of a predator-prey encounter

    Wang, L., Ruxton, G. D., Cornell, S. J., Speed, M. P. & Broom, M., 21 Jul 2019, In : Journal of Theoretical Biology. 473, p. 9-19 11 p.

    Research output: Contribution to journalArticle

  2. Spatial-stochastic modelling of synthetic gene regulatory networks

    Macnamara, C. K., Mitchell, E. & Chaplain, M. A. J., 10 Feb 2019, In : Journal of Theoretical Biology. In press

    Research output: Contribution to journalArticle

  3. Approximate Bayesian computation reveals the importance of repeated measurements for parameterising cell-based models of growing tissues

    Kursawe, J., Baker, R. E. & Fletcher, A. G., 14 Apr 2018, In : Journal of Theoretical Biology. 443, p. 66-81 16 p.

    Research output: Contribution to journalArticle

  4. Energy intake functions and energy budgets of ectotherms and endotherms derived from their ontogenetic growth in body mass and timing of sexual maturation

    Werner, J., Sfakianakis, N., Rendall, A. D. & Griebeler, E. M., 7 May 2018, In : Journal of Theoretical Biology. 444, p. 83-92 10 p.

    Research output: Contribution to journalArticle

ID: 244397967

Top