Combinatorial effects of multiple TFs distinguishes cell identities. (A) PCA showing TF expression across domains mirrors trends of genome-wide expression profiles with PC1 (red) and PC2 (blue) separating Tip and vasculature, respectively. PC3 (yellow) distinguishes the internode, and leaf primordia group together. (B) Mean TF family expression across domains correlates with given PCs. Examples are shown for TF families either positively (left) or negatively correlated (right) to PC1. Absolute correlation coefficients (│r│) are indicated. (V) Vasculature. (C) Overview of absolute correlation coefficients (│r│) for each TF family to each major PC. A threshold of 0.6 (dashed line) was used as a correlation cutoff. Mean expression of TF families shown in red is negatively correlated to meristem identity. (D) Diagrams illustrating that combined expression values for all TFs positively (green) and negatively correlated (red) to PC1 together can govern cell-type specificity (yellow). Gray, not examined. (E) Visualization of a GRN for select CZ-specific genes (yellow and blue) with combinatorial and hierarchical interactions from TF families positively (green) and negatively correlated (red) to PC1, as well as individual CZ-specific TFs (blue). (F) Percentage of CZ-specific genes with binding sites for PC1-correlated TF families in their promoter. The number of tested motifs is given in parentheses. TF families shown in red are negatively correlated to PC1. (G) Distribution of KN1-bound (dark orange) and KN1-bound and -modulated (light orange) targets among apex-expressed genes grouped into 20 bins based on SE score (right y-axis) shows KN1 primarily targets dynamically expressed genes. (Obs) Observed, (Exp) expected. (H) DEGs targeted by KN1 are preferentially expressed in organ primordia and vasculature. (n.s.) Not significant, (**) P < 0.01, (***) P < 0.001, based on χ2 test with Yates’ continuity correction.
