Gene Regulatory Network topology mediates the role of diffusible components in cellular patterns: the root epidermis of Arabidopsis thaliana as a study system

The differentiation of two cell types in the root epidermis of Arabidopsis thaliana-atrichoblasts, which give rise to hair cells, and atrichoblasts, which do not develop into hair cells-is orchestrated by a complex regulatory network of transcription factors and hormones. These elements synchronize spatially and temporally to create a characteristic interspersed pattern of hair and non-hair cells. Previous models have established a minimal regulatory network that captures the wild-type (WT) phenotype and some mutants, yet these models often fail to account for most mutant phenotypes, thereby limiting their predictive scope. In this study, we introduce an enhanced model, a diffusion-coupled regulatory genetic network, or meta-GRN, which extends our research group's previously published work. This model aims to describe the organizational patterns of the root epidermis more accurately. It successfully recovers, fully or partially, the phenotypes of loss-of-function mutants related to the identity regulators of epidermal cell types included within the model. Moreover, this expanded model quantitatively describes the distribution of trichoblasts and atrichoblasts relative to cortex cells, facilitating comparisons of cell type proportions at various positions against those reported in analyzed mutants. Crucially, the model highlights the role of diffusion processes in the lateral inhibition mechanism that governs network dynamics, underscoring their pivotal role in pattern formation in both the WT phenotype and various mutants.