Fig. 5. PROM1 is polycomb-repressed in CD133− leukemia cells.

a MLL-N, H3K79me2, H3K79me3, H3K27ac, H3K4me1, H3K4me3, H3K27me3 and EZH2 ChIP-seq, and ATAC-seq at PROM1 and TAPT1 in THP1 cells. H3K27me3 ChIP-seq at PROM1 and TAPT1 in SEM cells. b MLL-N, H3K27me3, and EZH2 ChIP-seq at PROM1 and TAPT1 in RCH-ACV cells. c Comparison of Capture-C tracks from the promoter of PROM1 and TAPT1 in SEM (black) and THP1 (red) cells. Gray bars show the Capture-C viewpoint. Tracks are the mean of three biological replicates. d Capture-C from the PROM1 and TAPT1 promoter in control (DMSO; black) and EPZ-5676-treated (DOT1Li; orange) THP1 cells. Differential tracks show the change in Capture-C signal (black: increases; red: decreases). Tracks represent the mean of three biological replicates. e Model for coregulation of PROM1 and TAPT1 expression. Left: in CD133-positive MLLr cells, the MLL fusion protein (MLL-FP) binds at the promoters of PROM1 and TAPT1 and spreads into the gene body. Recruitment of DOT1L results in elevated H3K79me2/3 levels, facilitating enhancer activity. These KEEs come into proximity with the promoters of both genes, upregulating expression of PROM1 and TAPT1. Right: in CD133-negative MLLr cells, PRC2 binding at the promoter of PROM1 generates a localized peak of H3K27me3 and disrupts MLL-FP binding at the promoter and gene body, repressing PROM1 expression. MLL-FP is still able to bind at the promoter of TAPT1, but for unknown reasons does not spread into the gene body. The lack of MLL-FP spreading within PROM1 and TAPT1 prevents the formation of KEEs, so the expression of neither gene is upregulated.