In Arabidopsis thaliana, cellular communication is mediated, among others, by plant hormones that belong to a limited variety in comparison with the types of developmental contexts in which they participate. For example, auxin is a plant hormone that can virtually participate in every developmental process, but how auxin responses become context-specific remains a matter of research. In the root, auxin has a gradient distribution with a maximum in the organizer of the root stem cell niche (SCN), where the expression of the transcription factor WOX5 is confined. The expression of WOX5 is key for the root SCN organizer identity and patterning, and experimental evidence has suggested that this transcription factor is both repressed and induced by auxin. To address this apparent paradox, we put forward a Boolean model that integrates the genetic and hormonal regulatory network, that may constitute a multi-stable system that underlies both types of WOX5 responses to auxin. We use this model to test the hypothesis that such regulatory network underlying cortical tissue specification, also control the expression of components of the auxin signaling pathway to prime these tissues for WOX5 expression. The model put forward here recovers the observed genetic configurations of the different cell types within the root SCN under wt and several mutants, and it provides a novel dynamic framework to predict the impact of undescribed perturbations that may alter the position of the SCN organizer. The modeling approach presented here, thus has enabled us to put forward a mechanistic explanation for the apparent paradoxical observations of auxin signaling both promoting and repressing WOX5 expression. Our model suggests that the final outcome depends on the tissue context in which the hormone is sensed.
