bioRxiv2025
Eukaryotic cells are spatially organized into functionally-distinct compartments. This three-dimensional(3D) organization generates intracellular heterogeneities that can modulate regulatory dynamics. Despite this knowledge of subcellular organization, most quantitative gene-regulation models still assume a well-mixed environment in which molecules can react regardless of their spatial positions. Here, we use the well-established galactose switch in budding yeast (Saccharomyces cerevisiae) to develop spatially-resolved models that integrate experimentally-derived intracellular architectures, including chromosome organization, the endoplasmic reticulum (ER) and spatially distinct ribosome populations. We implement a hybrid stochastic-deterministic framework in which gene expression is modeled using a reaction-diffusion master equation that enforces locality (i.e., reactions occur only when molecules are in physical proximity), while metabolic and transport processes are captured by ordinary differential equations. Guided by electron microscopy and biochemical constraints, we quantify how accounting for intracellular spatial organization alters regulatory predictions in the galactose switch. We show that chromosome geometry has little effect on Gal2p output, whereas ER-associated translation reduces Gal2p delivery to the plasma membrane; the largest decrease of Gal2p abundance occurs when translation of GAL2 mRNA is restricted to a population of ribosomes physically bound to the ER. Together, these results demonstrate that more realistic 3D cellular architectures and local reaction rules can qualitatively change regulatory predictions, motivating integration of intracellular organization in future whole-cell models. Author SummaryEukaryotic cells are highly organized spaces with distinct subcellular compartments and heterogeneous distributions of molecules which influence how cells function. Yet, most computational models of gene regulation assume a spatially homogeneous intracellular environment. To quantify how intracellular architecture influences regulatory predictions, we developed spatially resolved models of the galactose switch in budding yeast, a well-characterized gene regulatory system controlling the response to extracellular galactose. We compared conventional well-stirred simulations with models that explicitly incorporate experimentally informed intracellular organization, including chromosome positioning, endoplasmic reticulum geometry, and functionally distinct ribosome populations. Incorporating these spatial features substantially altered the dynamics of predicted gene activity, protein production, and intracellular sugar levels. Our results demonstrate that the three-dimensional organization of eukaryotic cells can significantly change regulatory outcomes of computational models, underscoring the need for integrating realistic spatial architectures in future models of eukaryotic gene regulation.