ERG expression in AML patients is proportional to the degree of H3K9/14Ac enrichment at the ERG promoters and +85 stem cell enhancer. (A) H3K9/14Ac enrichment across the ERG locus was measured in 26 AML samples by ChIP-chip. The enrichment profiles broadly fell into 4 visually recognizable patterns. Representative profiles of each pattern are shown below the Vista human/mouse sequence conservation (> 50%) plot. See supplemental Figure 1 for enrichment profiles in individual patients. (B) To group AML patients based on this epigenetic mark, 2 unsupervised clustering algorithms were used in conjunction with normalized H3K9/14Ac enrichments at the promoters and +85 stem cell enhancer. The panel to the left shows the hierarchical clustering pattern of patients together with a heat map representation of H3K9/14Ac enrichments. Sample IDs are listed to the left of the heat map and correspond to columns from left to right. The panel to the right shows the output of k-means clustering. The identity of patient samples in each group was the same irrespective of the clustering algorithm. (C) ERG transcripts in AML samples were measured by qRT-PCR and correlated with H3K9/K14Ac enrichment at the ERG promoter and +85 enhancer (right) using Mann-Whitney U test for statistical analysis. (D) Schematic diagram of the ERG locus (not to scale) showing the composite exon-intron structure of human ERG (upper). The translated exons are colored gray, and the positions of the promoter/enhancer elements relative to exons are indicated (the promoters as DP and PP and the +85 enhancer as a black bar). Exon usage of 2 transcripts originating from the distal promoter (Hs ERG2) and proximal promoter (Hs ERG3) are shown. (E) ERG transcripts originating from either the distal or proximal promoter were quantified. Their abundance is shown relative to total ERG in each AML sample.