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Background  Recent experimental work has uncovered some of the genetic components required to maintain the  Arabidopsis thaliana  root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes  SHORTROOT  and  SCARECROW  and the other depends on the  PLETHORA  genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of  WOX5  and  CLE40 , also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner.    Results  We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks.    Conclusions  These models are the first published approximations for a dynamic mechanism of the  A. thaliana  root SCN cellular pattering. Our model is useful to formally show that the data now available are not sufficient to fully reproduce root SCN organization and genetic profiles. We then highlight some experimental holes that remain to be studied and postulate some novel gene interactions. Finally, we suggest the existence of a generic dynamical motif that can be involved in both plant and animal SCN maintenance.

Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche