The Role of Energy Dissipation in Shaping Eukaryotic Transcriptional Regulation*

A mechanistic understanding of gene regulation is essential for quantitative control over gene expression. In prokaryotic systems, engineering rules were established via synergy between theory and experiments using model synthetic systems. However, a lack of interrelatable theoretical and experimental approaches have slowed progress in eukaryotes, where gene expression involves complex regulation driven by highly cooperative energy dissipative processes. To address this deficit, we developed a framework for modelling non-equilibrium regulation and used it to define underlying parameter regimes that set limits for cooperativity in various regulatory schemes, thereby discovering a trade-off between energy dissipation and cooperativity. To test our model, we developed an experimental system that enables sequence-level definition of a single-copy-integrated model fluorescent reporter locus in human cells. By expressing fluorescently labeled synthetic transcription factors—individually or in combination—that regulate the locus, we can precisely measure its gene regulatory functions. We envision using these theoretical and experimental approaches in tandem to establish quantitative rules for engineering complex gene networks in eukaryotes that incorporate non-equilibrium regulation.