Fig. 2: Spatial–temporal computer model of root cell proliferation for developmental control of G1.

a, Heat map showing enrichment of TF binding sites in rows, in the gene sets from each module (M1–M7, columns as defined in Extended Data Fig. 6). TF binding sites were mapped in 1-kb regions upstream of the transcription start sites as described in Methods, and fold enrichment on a log₂ scale was calculated by mapping the same sites in the complete Arabidopsis promoter set. b, Root tip of a plt1-4,plt2-2 double mutant in the PlaCCI marker line showing the reduced size of the RAM. Scale bar, 20 µm. c,d, Two representative frames of a video of the 35S::PLT2-GR line with the PlaCCI markers at 0 h (c) and 12 h (d) after treatment with Dex. Scale bar, 20 µm. e, Summary of G1 duration values in the wild type (taken from Fig. 1c and included here to facilitate comparison with the other genotypes). The shaded shape includes data of G1 < 20 h measured in the wild type. f, G1 duration in four root cell types (atrichoblasts, trichoblasts, cortex and endodermis; n = 36, 26, 81 and 64, respectively, from two roots), as indicated by the colour code, along the RAM in the plt1-4,plt2-2 double mutant. The shaded shape is the same as in e. g, G1 duration in four root cell types (atrichoblasts, trichoblasts, cortex and endodermis; n = 24, 19, 29 and 8, respectively, from four roots), as indicated by the colour code, along the RAM in the 35S::PLT2-GR line. The shaded shape is the same as in e and f. h, The IFFL mechanism underlying the model. The diagram shows the main elements taking part in the model and their connections. A high concentration of the driver in the root tip confers cell proliferation activity. In turn, the driver promotes the expression of the cell division regulator. Cell cycle phase length is inversely proportional to regulator amounts inside the cell. Thus, in the IFFL system the driver exerts a dual action stimulating cell proliferation and at the same time delaying cell cycle progression. i, Left: model simulation showing driver concentrations in the wild type. High concentrations of a growth regulator in the root tip induce the expression of the driver, which is allowed to diffuse along the meristem. Middle: model simulation showing regulator concentrations in the wild type. High driver concentrations in the root tip induce the expression of the regulator. Right: model simulation showing cell cycle time along the root as a result of regulator accumulation. j–l, Comparison between model simulation (light blue dots) and experimental data (red dots) in the wild type (j), the mutant with a reduction of driver expression (plt1-4,plt2-2 for experimental data; k) and the mutant with a constitutive driver expression (35S::PLT2-GR line for experimental data; l). Each dot represents the value relative to a single cell. The P value indicates the probability of obtaining a similar data fit from randomized simulations based on Hausdorff distance⁵¹ and the random sampling method. P < 0.05 indicates significant quantitative similarity between model predictions and experimental data (see the test description in ‘Computational model description’ in Methods).

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