Extended Data Fig. 5: Detailed profiling of H3K27me3 landscapes in MDA-MB-468 cells under 5-FU treatment.

All the experiments were performed in MDA-MB-468 cells. a. Schematic view of the experimental design used to analyze chromatin landscapes of persister and resistant cells. All samples were analyzed at the single cell level except 5-FU-D77-#3 and 5-FU-D113-#4. Samples used for bulk ChIP analysis are indicated with a black asterix. b. Histogram representing the frequency of epigenomic clusters within each sample. c. Scatterplot representing for each differentially enriched H3K27me3 peak, log2 expression FC versus log2 enrichment FC for the associated gene. Pearson’s correlation scores and associated p-value are indicated. d. Cumulative scH3K27me3 profiles over TGFB1 and FOXQ1 in resistant cells. e. Venn diagram representation of the region-based differential analysis performed to extract regions depleted in H3K27me3 jointly in E2/E1 compared to E4 (scChIP-seq dataset) f. Scatter plot representing log2 expression fold-change induced by 5-FU in resistant cells versus EZH2i-1 induced changes, and compared to the untreated population (D0). Pearson’s correlation scores and associated p-value are indicated. g. Doughnut plot displaying the fraction of 5-FU persister genes potentially regulated or not by H3K27me3 and expressed upon EZH2i-1 treatment. h. Heatmap representation of the targets of the three master TF among persister genes. Blue color stands for target genes while white means the gene is not a target. i. Mean rank of TF enrichment among persister genes obtained by ChEA3 for FOXQ1, FOSL1 and NR2F2 (red line) compared to the average mean rank in a 100 sets of random genes (green curve). j. Cumulative scH3K27me3 and scH3K4me3 enrichment profiles over FOSL1 and NR2F2 in untreated and persister MDA-MB-468 cells (D33 - H3K27me3 and D60 - H3K4me3). Log2FC for H3K27me3 and scRNA between persister and untreated populations are indicated.