Figure 2
The ERα reference cistrome (ERα-Ref) for MCF-7 cells. (a) Schematic representation of our strategy applied in the analysis of the ERα cistrome. (b) Bar plot reporting the ERα-Ref as divided by the experimental contexts or as a whole (fifth bar) and divided in co-occurrence subsets, i.e. ERBSs are classified in four subsets depending on whether they occur in a single context (C1), in two (C2), in three (C3) or in all the experimental contexts (C4) (increasing grey scale). At top of each bar, the number of ERBSs in each cistrome is reported. (c) Distribution of each context-specific cistrome (colors) into the C1–C4 subsets, inside each subset, ERBSs are ranked simply by their genomic coordinates. Red: E2-Independent; Orange: E2-Early; Green: E2-Late; Blue: E2-Constitutive; White: no binding detected. (d) Intensity heat map of a time-course ERα ChIP-Seq experiment performed in untreated or E2-treated MCF-7. (e) Box plot reporting for each time point, the distribution of average ERα ChIP-Seq read counts computed in a window of ±200 bp around ERBSs center. P-value from Mann-Kendall test considering the mean and the variance of each distribution. (f) Heat map reporting in blue the ERBSs overlapped with independent genomic features including: ERα bound active enhancers previously identified in MCF-7 (Active Enhancer), genomic regions of ERα-mediated long-range chromatin interactions (ChIA-PET), ERBSs identified in primary tumors from breast cancer patients who responded (R) or not (NR) to adjuvant treatment with Aromatase Inhibitor (AI) or Tamoxifen (Tam); ERBSs identified in distal breast cancer metastases; and the list of variants from iCOGS project. (g–h) Dot plot reporting, the average Pearson correlation coefficient computed between ERα ChIP signal and the signal of different TRs, chromatin accessibility signals measured by DNase-Seq experiment, and ChIP-Seq against ERα phosphorylation at Serine 118 (S118). The result for each ERα-Ref subset is reported.
