Figure 2

Absence of cognate partner in the SVP-FLC complex influences genome-wide binding events of individual transcription factors. (A) Number of significantly read-enriched peaks and their corresponding genes (left) for SVP binding in FLC (violet) and in flc-3 mutant genotype (blue). Overlap among target genes for both genotypes (right). (B) Number of significantly enriched peaks and their corresponding genes (left) for FLC binding in SVP (purple) and in svp-41 mutant genotype (blue) (left). Overlap among target genes for both genotypes (right). (C) Validation of selected targets. For each target, fold-enrichment relative to its input is shown. Plus signs indicate primers flanking predicted binding site; minus signs indicate primers not flanking predicted binding site used as negative control. Mean values are accompanied by standard error. (D) Top left: Venn diagram displaying the number of overlapping targets highly enriched for SVP binding in flc-3 mutant and highly enriched for FLC binding in svp-41 mutant ChIPs. Shared targets (total 87) are shown in the overlap area. Top right: Venn diagram displaying the number of overlapping targets highly enriched in ChIP for SVP binding only in WT and highly enriched for FLC binding only in WT ChIPs. Bottom: heat maps for a selection of 84 peaks for SVP binding in flc-3 mutant found to overlap the peaks for FLC binding in svp-41 mutant. Normalized binding signals are visualized 1.75 kb around each peak summit. The binding regions were sorted according to their maximum median value for FLC in the svp-41 mutant. (E) Heatmap of normalized binding signals for 148 peak summits corresponding to SVP binding in FLC WT that overlap the peaks found for SVP binding in flc-3 mutant (left), and for 170 peak summits corresponding to FLC binding in SVP WT and overlapping peak regions for FLC binding in svp-41 mutant (right). In both cases, results were sorted according to the maximum median values and visualized for genomic regions 750 bp around peak summits.