ChIP-seq for H3K4me and H3K27ac assigns potential enhancers to transcripts under control of HoxA9. (A) Metagene plot and occupation heat map of H3K4me and H3K27ac around all 24 470 identified HoxA9 peaks at 0 hours (Hox active) and 72 hours (Hox inactive). Heat maps are drawn for 0 hours only. H3K4me and H3K27ac profiles were determined in WT cells transformed by HA-tagged HoxA9. (B) HoxA9 coincides with H3K4me and H3K27ac at promoters and enhancers. The example covers the Myc gene and its known³²  enhancer ∼1.5 Mbp downstream. (C) Transcript response to HoxA9 correlates predominantly with H3K27ac in enhancers and promoters. Enhancer modifications change in response to HoxA9 activity (top panel). The situation at the Myc enhancer is shown at 0 hours (Hox on) and 72 hours (Hox off). HoxA9 ChIP, nascent RNA-seq, H3K27ac, and H3K4me IGV tracks are depicted. HoxA9 regulation allows association of enhancers with their cognate genes (middle panel). The example depicts the situation for Hmga2, in which a putative upstream enhancer is occupied and regulated by HoxA9. IGV tracks shown are as above. H3K27ac kinetics faithfully predicts HoxA9 activity (bottom panel). The intergenic region between Lcn2, a transcript repressed by HoxA9, and Ptges2, a gene bound, but not regulated, by HoxA9 is displayed. Please note that Ptges2 transcript abundances are too low to be visible in the RNA tracks at the scale necessary to visualize Lcn2 upregulation after inactivation of HoxA9. Potential promoter/enhancer sites are boxed. (D) Most HoxA9 sites are not involved in gene regulation. The Venn diagram depicts the numbers of acetylated regions changing modification density by ≥twofold 72 hours after inactivation of HoxA9 and the respective overlap with HoxA9 peaks.