Fig 1: Epigenomic heterogeneity of candidate enhancers bound by Fra-1 and/or Fra-2. (A) Heatmaps of ATAC-seq (53) and ChIP-seq signals in MDA-MB-231 cells cultured under standard conditions at ±1 kb around PF1, F1F2 and PF2 peak centers at candidate active enhancers (cAEs; upper panel) and candidate inactive enhancers (cIEs; lower panel). Regions were sorted according to Fra-1 decreasing signal intensity and the number of regions in each category is indicated on the left. (B) Comparison of ChIP-seq metaprofiles for Fra-1, Fra-2 and p300/CBP at PF1, F1F2 and PF2 peaks between cAEs (green) and cIEs (orange). (C) p300/CBP recruitment at F1F2 peaks in cAEs upon Fra-1 siRNA-mediated knockdown. The left panels represent the ChIP-seq metaprofiles of p300/CBP at ±1.5 kb around F1F2 peak centers in cAEs of MDA-MB-231 cells transfected with either siCTL or siFra-1 for 72h. Regions were sorted according to the p300/CBP signal-fold change in siFra-1- versus siCTL condition. The threshold was set up to ±1.5, defining three types of regions: regions with -1.5 < FC < 1.5, FC = 1.5 and FC = -1.5. Middle panels represent screen captures of the ChIP-seq profiles of peaks representative of each category of regions using the IGV software. The screen captures correspond to peaks A, D and I, which were analyzed by ChIP-qPCR, as presented in the right panels. These ChIP-qPCR experiments were carried out on MDA-MB-231 cells transfected with either siCTL, siFra-1 or siFra-2 (right panels). Three regions per category were tested: A, B and C are regions with -1.5 < FC <1.5; D, E and F are regions with FC = +1.5 and G, H and I are regions with FC = -0.5. Signals were normalized to inputs and to the siCTL condition set to 1 for each amplicon. Results are the mean of five independent experiments. P-values were calculated using a two-tailed unpaired t-test (Prism5 software). (*), (**), (***) and (****) correspond to P-values of =0.05, = 0.01, = 0.005 and = 0.0001, respectively. Coordinates of the regions analyzed and sequences of the primers used are given in Supplementary Data S1H.