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Fine-grained modelling of ATP dependence of decision-making capacity in genetic regulatory networks

Kumar, R.; Johnston, I.

2023-11-17 systems biology
10.1101/2023.11.16.567352 bioRxiv
Show abstract

Cellular decision-making is fundamental to life, from developmental biology to environmental responses and antimicrobial resistance. Many regulatory processes that drive cellular decisions rely on gene expression, which requires energy in the form of ATP. As even genetically identical cells can have dramatically different ATP levels, bioenergetic status can be an important source of variability in cellular decision-making. Existing studies have investigated this energy dependence but often use coarse-grained modelling approaches (which are not always readily connected to the underlying molecular processes of gene regulation). Here we use a fine-grained mathematical model of gene expression in a two-gene decision-making regulatory network to explore cellular decision-making capacity as energy availability varies. We simulate both a deterministic model, to explore the emergence of different cell fate attractors as ATP levels vary, and a stochastic case to explore how ATP influences the noisy dynamics of stochastic cell decision-making. Higher energy levels typically support increased decision-making capacity (higher numbers of, and more separated, cell states that can be selected), and the fine-grained modelling reveals some differences in behaviour from previous coarse-grained modelling approaches.

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