Figure 7. Changes in chromatin organization in mitochondrial, oxidative phosphorylation and amino acid metabolism genes.
Shift in NFR occupancy in re-wired respiratory genes (A and B). Shown are the logarithm of the p value of the KS-test (y axis) used to test if the genes in a given set (mitochondrial genes, A, and oxidative phosphorylation genes, B) have a significantly lower nucleosome occupancy at their 5′NFRs than that of all genome genes in each of 13 species (x axis) with nucleosome positioning data from Tsankov et al. (2010) and Xu et al. (2012). (C) Evolutionary repositioning of binding sites for key amino acid TFs relative to NFRs. For each of 13 species (columns, tree), shown are the enrichment (yellow) or depletion (blue) in NFRs of binding sites for several amino acid and purine metabolism TFs (rows) whose sites are depleted from NFRs in post-WGD species and enriched in pre-WGD species. The intensity of the color is proportional to the z-score estimated for each regulator from the fraction of all its binding sites that are in the NFR. Each row is centered by its mean value (see ‘Materials and methods’).