Extended Data Fig. 6: Analysis of H3K4me3 and H3K4me3/H3K27me3 enrichment in untreated cells.
From: H3K27me3 conditions chemotolerance in triple-negative breast cancer

a. Heatmap representation of single-cell H3K4me3 enrichment at H3K27me3-regulated persister genes, non-expressed protein coding genes and housekeeping genes in untreated cells (D0) and persister cells (D60). b. Violin plots representing the distribution of percentage of cells with H3K4me3 signal across H3K27me3-regulated persister genes, non-expressed protein coding genes and housekeeping genes, compared with a one-sided Wilcoxon rank text. c. Violin plot representing the distribution of percentage of H3K27me3-regulated persister genes with H3K4me3 signal in untreated cells (D0) and persister cells (D60). One-sided Wilcoxon rank test is used for the comparison between the two conditions d. (Up) Cumulative scH3K4me3 profiles over the TGFB1 locus between untreated cells (D0) and persister cells (D60). (Down) H3K27me3->H3K4me3 and H3K27me3->IgG sequential ChIP-seq profiles of TGFB1 in the untreated population. Comparative tracks show enrichment over IgG control with associated odd ratio and q-value. e-f. Dot plot of the number of false positive peaks detected (with IgG) for each number of bivalent peaks detected at various enrichment and q-values, assessed with one-sided Fisher’s exact test, adjusted for multiple testing. Used thresholds are indicated in red. g. Venn diagram of MDA-MB-468 bivalent genes found by sequential ChIP-seq in the H3K4me3-H3k27me3 way, the H3K27me3-H3K4me3 way. The enrichment of the intersection between the two ways is tested using a Fisher’s exact test. h. Dotplot of the -log10(q-value) of bivalent pathways (as in g.) in the H3K4me3-H3K27me3 and the H3K27me3-H3K4me3 ways. i. (Left) Barplot displaying the top 5 pathways enriched in H3K27me3/H3K4me3 bivalent genes identified in untreated cells in MDA-MB-468, BT20 and HCC38. X-axis corresponds to -log10 q-values. (Right) Venn diagram displaying the intersection of the pathways enriched in H3K27me3/H3K4me3 bivalent genes identified in the untreated cells. P-value corresponds to the significativity of the overlap calculated with Exact Test of Multi-set Intersections.