Fig. 3: PIF4 and CDF2 bind to overlapping genomic targets and cooperatively regulate their expression. | Nature Plants

Fig. 3: PIF4 and CDF2 bind to overlapping genomic targets and cooperatively regulate their expression.

From: PIF4 enhances DNA binding of CDF2 to co-regulate target gene expression and promote Arabidopsis hypocotyl cell elongation

Fig. 3

a, Positional distribution of CDF2 ChIP–seq peaks relative to the gene body. The observed distribution (black), the 95% confidence interval (shaded blue) and mean (dashed line) of 1,000 random peak sets are shown. b, Position distribution of G-box motifs relative to the CDF2 ChIP–seq peak centres. c, Position distribution of DOF-binding motifs relative to the centre of CDF2 ChIP–seq peaks. d, Frequency distribution of the number of G-box motifs observed in CDF2 ChIP–seq peaks. e, Density plots of the distance between consecutive G-box motifs in the observed CDF2 ChIP–seq peaks (blue) and the promoters of all non-CDF2 targets (red). f, Frequency distribution of the number of DOF motifs observed in CDF2 ChIP–seq peaks. g, Density of the distances between consecutive DOF motifs in observed CDF2 ChIP–seq peaks (blue) and the promoters of non-CDF2 targets (red). h, Overlap between target genes of CDF2 and PIF4. i, Density plot showing the distribution of distances between PIF4 and CDF2 ChIP–seq peaks. j, Positional distribution of G-box motifs relative to centres of PIF4/CDF2 common ChIP–seq peaks. k, Frequency of G-box motifs observed in ChIP–seq peaks shared between PIF4 and CDF2. l, Density distribution of the distances between consecutive G-box motifs in ChIP–seq peaks common to the PIF4 and CDF2 peak sets (blue). The distribution is compared with that obtained by examining the promoters of all non-targets (red). m, Volcano plot describing the differential binding analysis of DiffBind package, by plotting the log2 fold change in binding strength against the −log10 P value of the differential binding test. The confidence threshold: false discovery rate ≤ 0.05. n, Venn diagram consistency in the direction of gene expression change in cdfQ and pif4 mutants relative to that in Col-0. o,p, Heatmap showing the z-score normalized expression values of selected genes in the cotyledon (o) and hypocotyl (p) of Col-0, cdfQ and pif4-2 mutants.

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