Extended Data Fig. 9 |. Immune gene activation associated with the mesenchymal state is epigenetically regulated.

a, ChIP-qPCR analysis of the indicated histone marks at the indicated immune gene promoters in SH-SY5Y cells expressing dox-inducible PRRX1 ± dox. Data points represent mean of 2 technical replicates of 2 independent experiments. Enrichments at TAP1 and PSMB9 loci represent the data corresponding to amplicons 4 and 6, respectively, in Fig. 4a. b, Enhancer regions in 5Y-par., 5Y-res. and SH-EP cells. H3K27ac bound regions identified as significant peaks were stitched together if they were within 12.5 kb of each other (typical enhancers; grey). SEs (red) were defined as stitched enhancers surpassing the threshold signal based on the inclination point in all cell types. In 5Y-par., 5Y-res. and SH-EP cells, 2.94% (915/31116), 6.56% (1880/28635) and 4.18% (1215/29057) of the enhancers were classified as SEs, respectively. The top five SE-associated lineage-specific genes are highlighted. c, ChIP-qPCR analysis of EZH2 and SUZ12 enrichment at the indicated immune genes in 5Y-par. cells. Negative control loci, PHOX2B and LIN28B. Data represent mean of n = 2 independent experiments. d, e, Scatter plots representing the differential binding of the indicated histone marks at the promoter regions of all protein coding genes between 5Y-par and 5Y-res. (d), and 5Y-par. and SH-EP cells (e). rpm/bp, reads per million per base pair. A ≥ 0.75 log₂FC threshold was used to identify unique peaks for each histone mark. f, Bar plots representing the numbers of immune genes with increased promoter deposition of H3K4me3 and H3K27ac (log₂ FC ≥ 0.75) and loss of H3K27me3 (log₂ FC ≥ 0.75) marks, together with increased RNA expression (log₂ FC ≥ 1) in 5Y-res. (left) or SH-EP (right) compared to 5Y-par. cells. g, Violin plots of the ratios of active to repressive histone marks surrounding immune gene promoters in the indicated cells. Significance determined by the two-tailed Wilcoxon rank-sum test. Box plots within the violin plots defined by center lines (medians), box limits (25^th and 75^th percentiles) and whiskers (minima and maxima; 1.5X the interquartile range).