Fig. 5: Differential C/EBPB occupancy regulates extracellular matrix organization.

a, b Total number of upregulated (a) and downregulated (b) C/EBPB binding sites in adapted (n = 3) MDA-MB-231 cells relative to the parental (n = 3) using DiffBind with an FDR < 0.05 (The p-values were determined using default binomial distribution in HOMER). Unique gain or loss sites refer to binding sites identified only in the adapted or parental condition, whereas shared peaks are peaks called in both conditions. Top 5 significant de novo motifs enriched in the unique gain or loss sites were called by HOMER. c Metagene representation of the mean C/EBPB Cut&Run signal (fragment length ≤120 bp) across the same chromatin regions as in open ATACseq peak enriched in adapted cells from three biological replicates of adapted or parental MDA-MB-231 cells. Control IgG Cut&Run experiment in adapted and parental cells was included for comparison. d Representative genome browser tracks of normalized C/EBPB and IgG Cut&Run and ATACseq profiles around the LCN2 locus in biological replicates of parental and adapted MDA-MB-231 cells. e Reactome pathway analysis of genes containing gained chromatin accessibility to C/EBPB. f Heatmaps showing average Cut&Run and ATACseq signal intensity centered around the transcription start site (TSS) of the nine putative C/EBPB target genes, and the corresponding mRNA expression of the same genes in three biological replicates of MDApar and MDAapa cells (panels 1–5). Heatmap of expression fold change of the same genes in obese and overweight compared to lean patients was also shown (panel 6). g Heat map showing mRNA expression of potential C/EBPB targets in E0771 cells isolated from chow diet and HFD-fed mice. mRNA expression was measured by RT-qPCR with cells isolated from n = 2 chow tumors and n = 3 HFD tumors. Source data are provided as a Source data file.