A subset of MLL-ENL–bound genes exhibits aberrant H3K79 methylation and differential gene expression. (A) Identification of genes with differential methylation level of H3K79 in MLL-ENL activated and inactivated conditions. The level of H3K79 methylation under 4-OHT and no 4-OHT conditions is plotted for each of 16 644 genes tiled on the array. Blue dots represent 2568 H3K79 target genes identified in the MLL-ENL inactivated condition. Green dots indicate the subset of H3K79 target genes that show differential methylation level of this histone modification (FDR < 0.25). Green dots above the diagonal line represent the 40 genes with significantly higher level of H3K79 methylation in the MLL-ENL–induced condition (FDR < 0.25) that are referred to as H3K79High_4HT genes. The green dots below the diagonal line represent the 20 genes with significantly increased levels of H3K79 methylation when MLL-ENL was inactivated (FDR < 0.25), that are referred to as H3K79High_no4HT genes. (B) The set of 223 MLL-ENL–bound genes (Figure 4B) is compared with differentially up-regulated genes (panel D) and genes with higher level of H3K79 methylation (Figure 5A) in the MLL-ENL–induced condition. The shaded area indicates 12 MLL-ENL–bound genes with differential expression. (C) Correlation between MLL differential binding and differential H3K79 methylation. For each MLL target gene, the difference in MLL binding strength and the differences in the level of H3K79 methylation between 4-OHT and no 4-OHT conditions were calculated. Red dots represent 223 MLL-ENL target genes (Figure 4B), with the red line showing the regression line of MLL binding difference to methylation difference for 223 MLL-ENL target genes (Pearson correlation, r = 0.69). Green dots are 2513 MLL wild-type–bound genes eliminating 223 MLL-ENL target genes, with the green line showing the regression line (Pearson correlation, r = 0.27). (D) Identification of 12 MLL fusion-regulated genes. Average gene expression is plotted against the difference in gene expression between MLL-ENL induced and inactivated conditions. All 7858 expressed genes detected by Affymetrix Mouse Exon 1.0 ST Array are displayed. Blue dots represent 124 differentially expressed genes (67 up-regulated, 57 down-regulated, FDR < 0.05) on induction of MLL-ENL. The set of 223 MLL fusion-bound genes, shown as the red dots, are overlaid with 124 differentially expressed genes, and the overlapped blue and red dots indicate 12 MLL fusion target genes exhibiting significant increase in mRNA expression in the presence of MLL-ENL.