Applying Terrific, we identified that about 77 in the genes linked with active TFAP2A peaks are also related with active MITF peaks, a very important SB-431542 overlap (hypergeometric test, p0.0001) (Fig 3D). In addition, 79 of those genes are connected with active TFAP2A/ MITF shared peaks, suggesting that TFAP2A and MITF are co-bound at quite a few, but not all, shared targets. GO term analysis [76,77] revealed that the subset of genes linked with each TFAP2A and MITF peaks are enriched for the terms “melanosome” and “pigment granule” (p = 9.08E-07), at the same time as “DNA repair” (p = 5.98E-08), “mitotic cell cycle process” (p = 5.59E09), “regulation of cell proliferation” (p = two.40E-03), and “regulation of cell differentiation” (p = two.60E-03) (all p-values Bonferroni corrected, S9 Table). This supports a regulatory function for TFAP2A not merely in differentiation, but across other categories of genes proposed to be regulated by MITF in melanocytes and melanoma, as with all the MITF rheostat [22]. To assess the overlap amongst targets of TFAP2A and MITF with respect to pigmentation, we focused on a list of 170 genes that cause coat color phenotypes in mice [78], adding TRPM1 according to its function inside the coat colour phenotype of appaloosa horses [792]. Orthologs of 97 genes on this list are related with active TFAP2A peaks in human melanocytes and/or active TFAP2A peaks in mouse melanocytes (Table 1, asterisks). Of those, 72 genes are also linked with active MITF peaks (Table 1), 46 becoming active shared TFAP2A/MITF peaks (Table 1, bold). We then examined overlap of MITF and TFAP2A binding at clusters of closely spaced enhancers, from time to time referred to as stretch or super-enhancers (SEs) [83], which can be linked to cell type-specific gene expression [84,85]. Following published methods, we utilized H3K27ac data to identify 652 SEs in human main melanocytes [85] (S7 Fig). Of those, 530 (81 ) are bound by each MITF and TFAP2A (Fig 3E, S10 Table). Interestingly, genes involved in melanocyte differentiation, like these encoding proteins expressed inside the melanosome, are linked with SEs bound by MITF only (e.g. TYR, MLANA, SLC24A5, DCT) and SEs bound by both MITF and TFAP2A (MLPH, OCA2, TRPM1, MC1R). Exceptions to this pattern consist of KIT, which is associated with a single SE bound solely by TFAP2A and one particular SE bound solely by MITF, and TYRP1, which can be related with an SE bound by neither (Fig 3E). Taken together, these results show that TFAP2A and MITF bind regulatory components associated with melanocyte differentiation effectors. Notably, 409 (63 ) of all SEs are bound by TFAP2A peaks that overlap with MITF peaks. It remains to be determined regardless of whether TFAP2A and MITF exhibit cooperative binding at these loci. Even though several from the pigmentation genes associated with active TFAP2A and MITF peaks showed TFAP2A-dependent expression in each zebrafish and mouse, we also noted numerous apparently TFAP2A-independent genes on this list. A single doable explanation is that the presence of a TFAP2A peak will not signify contribution of TFAP2A to the activity of a provided regulatory element. These results show that TFAP2A straight activates the TRPM1 promoter, supporting the hypothesis that other TFAP2 paralogs are able to compensate for the abse.