Figure 6.

SIZ1 affects the expression of SIM-induced shoot meristem genes. A, Heatmap showing transcriptional regulators up-regulated in siz1-2 that are highly expressed during SIM incubation and also known to be involved in regeneration according to Ikeuchi et al. (2019). Normalized expression was calculated for each gene across all time points, using data from both genotypes. B, Relative expression in siz1-2 versus wild type (WT) plants of selected shoot meristem genes from the heatmap in A. Error bars represent ± SE. Asterisks indicate significant differences by edgeR comparative analysis between wild type and siz1-2 (*P < 0.05). C, Expression of the gWUS-GFP₃ reporter (green), visualized using confocal microscopy, in siz1-3 and wild-type hypocotyl explants after 4 d on CIM followed by 6 d on SIM. Samples were stained with propidium iodide (magenta) to stain cell walls. Scale bars = 50 µm. D, Quantification of the number of gWUS-GFP₃-expressing foci after 6 d on SIM, observed as in C. Sample sizes are wild type (n = 33) and siz1-3 (n = 36). Significance was tested with two-tailed Welch’s t test (*P = 2.9e−7) and error bars represent ± SE. E, Venn diagram showing the overlap between cytokinin-inducible genes and SIM-inducible genes. The list of cytokinin-induced genes was created by combining data from Nemhauser et al. (2006; 332 genes), Bhargava et al. (2013; 422 genes), and AtGeneExpress (ExpressionSet: 1008031453; 60 genes). SIM-inducible genes are those up-regulated in the wild type after 4 or 6 d of incubation on SIM compared to after cutting, based on our RNA-seq data (edgeR, false discovery rate [FDR] < 0.01). The significance of overlap between pairs of gene sets was evaluated by a hypergeometric test. The calculated representation factor is shown in brackets. F, Heatmap showing the expression of genes which are both cytokinin inducible and SIM inducible, as identified in E, in siz1-2 and wild-type plants. Differentially expressed genes (DEG) are marked in red for up-regulated genes in siz1-2 at SIM 4 d or 6 d and in blue for down-regulated genes.