Fig. 4

BAF60 preferentially associates with G-box motifs and shares a large repertoire of target genes with PIF4. a HOMER motif search identifies a major BAF60-associated motif defined as the G-box (CACGTG). P value = 1e-296. b Venn diagram representing the overlap between BAF60 target genes and genes containing a G-box motif in their promoter (500-bp upstream domains). c Venn diagram representing the overlap between BAF60 and PIF4 target genes. d Density plot showing overlap of PIF4 and BAF60 using hexagonal binning routine. As a large number of data points may overlap, hexagonal binning gives an additional dimension of differentiation of overlapping points based on count. Each point represents the distance of the midpoint of a peak to the nearest gene. On the y-axis is the location of the midpoint of a PIF4 peak in comparison to gene position; on the x-axis is the location of a midpoint of BAF60 in comparison to the nearest gene. A large number of points occurs along the positive correlation line, showing the co-occurrence pattern of PIF4 and BAF60. e Genome Browser snapshots of BAF60 (green) and PIF4 (red) ChIP-seq peaks on two representative genomic regions of chromosome 4 [chr4:10,235,000–10,361,000] (left) and chromosome 1 [chr1:28,285,000–28,381,000] (right). Genes are shown in black and G-boxes in pink. f Venn diagram representing the overlap between the BAF60 targets, found through ChIP-seq, and the missregulated genes in the Baf60 RNAi lines. The values in parentheses (grey) correspond to the common elements expected by chance, while those in black or red represent the observed results. The values in red represent significant enrichment, while those in black are not significantly different from those expected by chance (Chi-squared test). g Venn diagram representing common missregulated genes in the Baf60 RNAi line and the pifq mutant. The values in parentheses (grey) correspond to the common elements expected by chance, while those in black or red represent the observed results. The values in red represent significant enrichment, while those in black are not significantly different from those expected by chance (Chi- squared test)