Figure 2

Developmental dynamics of MADS-domain TF-bound genomic regions. (A) Proportion of overlapping AP1 or SEP3 BSs between time points depending on their rank (1 = highest rank). Only peaks near genes (3 kb upstream to 1 kb downstream of the gene) were considered. (B) Changes in AP1 and SEP3 BSs between consecutive time points. ‘Increasing peaks’ and ‘decreasing peaks’ are genomic regions with a peak score at least two-fold higher or two-fold lower, respectively, when compared with the previous time point. Only significant peaks (FDR <0.001) near genes in at least one time point are considered. (C) Summary of AP1 and SEP3 BSs at GRF loci. Each locus has a number of columns depending on the number of different AP1 or SEP3 BSs at any time point. For each column, ‘–’ indicates that the region was not bound and ‘+’ that it was bound (FDR <0.001); two consecutive time points are colored in gray when the ChIP-seq score of the earlier time point is at least two-fold higher than at the later time point and in blue when it is two-fold lower. (D) Floral phenotypes of plants expressing miRNA396 from the 35S or pANT promoter. One sepal and petal were removed for visualization. Arrow indicates petal-stamen organs, asterisk indicates conversion of floral organs into filament, arrowhead indicates ovary composed of a single valve in mutant flowers. In the column chart, data are represented as means, 100 flowers of each genotype were assessed. *** indicates significant difference at P value <0.001 by unpaired Student’s t test. (E) Mean change of log10 fold expression of genes in vicinity (up to 1 kb upstream of start or inside the gene) of different classes of AP1- and SEP3-bound genomic regions. Only differentially expressed genes were used (Additional file 7: Table S4). Bars correspond to standard error of mean.