A Practical Step-by-Step Guide for Quantifying Retroactivity in Gene Networks

Methods Mol Biol. 2021:2229:293-311. doi: 10.1007/978-1-0716-1032-9_14.


One of the fundamental properties of engineered large-scale complex systems is modularity. In synthetic biology, genetic parts exhibit context-dependent behavior. Here, we describe and quantify a major source of such behavior: retroactivity. In particular, we provide a step-by-step guide for characterizing retroactivity to restore the modular description of genetic modules. Additionally, we also discuss how retroactivity can be leveraged to quantify and maximize robustness to perturbations due to interconnection of genetic modules.

Keywords: Context-dependence; Gene transcription networks; Loading; Model order reduction; Modularity; Retroactivity; Synthetic biology.

MeSH terms

  • Algorithms
  • Computer Simulation
  • Gene Regulatory Networks*
  • Models, Biological
  • Synthetic Biology
  • Systems Biology / methods*
  • Transcription, Genetic