Fig. 4: MAF chromatin binding overlaps with and expands binding of ER.
From: MAF amplification licenses ERα through epigenetic remodelling to drive breast cancer metastasis
a, ER and MAF ChIP-seq peaks in control and MAF-overexpressing MCF7 cells that were HD or E2-treated (for 1 h). Groups of binding sites are defined based on the positional overlap between ER and MAF binding. Colour scale bars indicate the scale for Reads Per Genome Content (RPGC) normalized coverage (deepTools58). The number of peaks is indicated for each group. b, Shared MAF/ER binding sites from a are divided into common and increased ER binding sites in the presence of E2 (ER E2-gained) or in the presence of E2 and MAF overexpression (ER MAF/E2-gained). c, UCSC genome browser (http://genome.ucsc.edu, February 2009 (GRCh37/hg19)) screenshots of ChIP-seq profiles at representative target genes, showing ER ChIP-seq tracks from control and MAF-overexpressing MCF7 cells, either HD or E2-treated. p300 ChIP-seq peaks (from ref. 40) depict active enhancer regions. MAF ChIP-seq tracks from MAF-overexpressing MCF7 cells under HD conditions are shown. Predicted MAF binding sites (using the MAF or MARE matrices) within ER peaks are represented in black. bs, binding sites. d, Venn diagrams showing the overlap between p300 and ER binding sites in control (left) or MAF-overexpressing MCF7 cells (right) after E2 treatment. e, qRT–PCR expression analysis of PTHLH (left) and JAG1 (right) in control (mock-infected < yellow/orange) and MAF-overexpressing (blue/purple) MCF7 cells transduced with a lenti-dCas9-KRAB and a lentiGuide-puro expressing sgScramble (dark) or specific sgRNAs against PTHLH and JAG1 herein uncovered enhancer sequences (light). Cells were cultured under HD conditions and stimulated with 10 nM E2. Expression was normalized to the housekeeping gene B2M. n = 5 (PTHLH) and n = 6 (JAG1) biological replicates. Data are presented as mean ± s.e.m. P values were calculated using a one-sided t-test. f, Circos plot summarizing the chromosomal distribution of ER ChIP-seq reads in control or MAF-overexpressing MCF7 cells under HD conditions and after E2 treatment (10 nM, 1 h). The outermost circle represents the ideograms of each chromosome with labels in Mb of physical distance. The inner two circles show the density of ER ChIP-seq reads.
