Fig. 1: PHB and CNA have hundreds of uniquely regulated targets despite extensive overlap in genomic occupancy.
From: START domains generate paralog-specific regulons from a single network architecture
a Phylogenetic tree of the HD-ZIPIII family in A. thaliana (blue = REV subclade, red = CNA subclade). Tree rooted to the K. nitens HD-ZIPIII protein (KnC3HDZ, yellow). b Histograms and heatmaps of ChIP-seq signal intensities compared to a non-transgenic control. Histogram lines and colors delineate five categories of binding sites: CNA specifically bound (red, solid); mutually bound – CNA higher affinity (red, dashed); mutually bound – equal affinities (purple); mutually bound – PHB higher affinity (blue, dashed), and PHB specifically bound (blue, solid). Heatmaps are separated into three major categories: CNA uniquely bound (top), mutually bound (center), and PHB uniquely bound (lower). Mutually bound heatmaps contain three further subcategories: mutually bound – CNA higher affinity (top); mutually bound – equal affinities (center); mutually bound – PHB higher affinity (lower). c Venn diagram of sites bound by CNA and PHB. d Venn diagram of genes bound by CNA and PHB. e Venn diagram of direct targets of CNA and PHB, i.e. bound in ChIP-seq and differentially expressed in RNA-seq. Numbers in parentheses correspond to direct targets bound specifically by CNA or PHB. f Scatterplot showing differential expression of genes bound and regulated by both CNA and PHB. g Scatterplot showing differential expression of genes bound by both paralogs but uniquely regulated by CNA (red) or PHB (blue). h, i Representative genome browser shots illustrating differential usage of shared binding sites: AT2G22860 is bound by both paralogs but uniquely regulated by CNA (h), while AT3G19895 is bound by both paralogs but uniquely regulated by PHB (i).
