Fig. 3: PROM1 is regulated by H3K79me2/3-marked enhancers.

a Capture-C tracks from the viewpoint (gray bars) of the PROM1 and TAPT1 promoter in SEM and RS4;11 cells. ChIP-seq tracks for MLL-N, H3K79me3, H3K27ac, H3K4me1, and H3K4me3, and ATAC-seq at PROM1 and TAPT1 in SEM cells, and for MLL-N, H3K79me2, H3K27ac, and H3K4me1, and ATAC-seq at PROM1 and TAPT1 in RS4;11 cells. Putative enhancer regions are highlighted in blue. b H3K79me3, H3K27ac, H3K4me1 and H3K4me3 ChIP-seq, and ATAC-seq from bone marrow of a child with MLL-AF4 ALL. CD133 expression profile of these cells is shown in Supplementary Fig. 1e (upper panels). Putative enhancer regions are highlighted in blue. c Model for the structure of the PROM1/TAPT1 locus, based on Capture-C data. d ATAC-seq and H3K27ac ChIP-seq at PROM1 and TAPT1 in control (DMSO; orange/green) and EPZ-5676-treated (DOT1Li; gray) SEM cells. Statistically significant decreases in ATAC-seq peaks following DOT1Li are indicated by blue asterisks (FDR < 0.05 from three biological replicates). Histograms show overlay of ATAC-seq and H3K27ac ChIP-seq read counts across the highlighted regions. e ATAC-seq in control (DMSO; orange) and EPZ-5676-treated (DOT1Li; gray) RS4;11 cells. Histograms represent overlay of ATAC-seq read counts across the highlighted regions.