Sociated with TFAP2A peaks in mouse and human melanocytes, with

Sociated with Nts, an observation that supports the idea that {rare TFAP2A peaks in mouse and human melanocytes, with an assignment rule of basal promoter plus 100kb distal, and discovered that these genes are enriched for ontology terms relevant to melanocyte differentiation, including "pigmentation", "melanosome", and "melanoma" (S6A and S6B Fig). These genes are candidates to be direct transcriptional targets of TFAP2A, suggesting that the phenotype of delayed melanization in zebrafish tfap2a-/- mutantsPLOS Genetics | DOI:10.1371/journal.pgen.1006636 March 1,eight /TFAP2 paralogs regulate melanocyte differentiation in parallel with MITFFig 3. TFAP2A peaks are connected with genes involved in pigmentation. (A-C) Density-based clustering of H3K27ac signal at (A) TFAP2A peaks, (B) MITF peaks, and (C) TFAP2A peaks that overlap MITF peaks in human melanocytes (H3K27ac data from GSM1127072 [64]), MITF peaks from [18]). (D) Overlap among genes associated with active TFAP2A peaks and genes related with active MITF peaks in human melanocytes. (E) Common enhancers (gray) and super-enhancers (colored) in human melanocytes that overlap neither TFAP2A nor MITF peaks, TFAP2A peaks only, MITF peaks only, or each TFAP2A and MITF peaks. Labels determine melanocyte genes of interest. (F) Diagram from the TRPM1 -700 bp promoter element depicting the positions of four TFAP2A binding sites (A1 4) and the previously reported E-box 1 MITF binding web page (E1). (G) Luciferase assays in M21 melanoma cells. Deletion of all 4 TFAP2A binding web pages (AP2) considerably lowered reporter activity in comparison with the intact TRPM1 -700bp element (Student's t-test, p = 0.01). doi:10.1371/journal.pgen.1006636.gcan be explained in part by a direct effect on specific melanocyte differentiation effector genes (e.g., dct, mlpha, mc1r, and pmela), and indirect regulation of other people (e.g., slc24a5 and tyr).TFAP2A and MITF co-occupy regulatory elements connected with pigmentation genesThe presence of TFAP2A peaks at a majority of active melanocyte enhancers, also as the enrichment of the MITF binding motif in TFAP2A peaks, implies that TFAP2A binds several ofPLOS Genetics | DOI:10.1371/journal.pgen.1006636 March 1,9 /TFAP2 paralogs regulate melanocyte differentiation in parallel with Ative trait locus (eQTL) within a {large MITFthe same regulatory elements as MITF in melanocytes. To evaluate overlap among TFAP2A and MITF across the genome, we compared our human TFAP2A ChIP-seq results to a set of 16,572 MITF ChIP-seq peaks also from human primary melanocytes [18]. five,367 (39 ) of TFAP2A peaks are shared.Sociated with TFAP2A peaks in mouse and human melanocytes, with an assignment rule of basal promoter plus 100kb distal, and identified that these genes are enriched for ontology terms relevant to melanocyte differentiation, including "pigmentation", "melanosome", and "melanoma" (S6A and S6B Fig). Even so, TFAP2A can each activate and repress gene expression [73]. To find genes probably to be activated by TFAP2A, we integrated our TFAP2A ChIP-seq with H3K27ac ChIP-seq information from human melanocytes (GSM1127072 [64]) and mouse melanocytes [14], as H3K27ac marks active regulatory components [reviewed in 74,75]. We discovered that 55 of TFAP2A peaks in human melanocytes and 58 of TFAP2A peaks in mouse melanocytes either overlap H3K27ac peaks or are flanked by H3K27ac peaks, and we refer to them hereafter as active TFAP2A peaks (human Fig 3A, mouse S6C Fig, S7 Table).