Identification of PML-RARα–associated chromatin modifications. The dot plots on the right indicate the changes in histone modifications and HDAC1 binding in promoters bound by PML-RARα. To allow comparisons, the panels on the left show promoters with altered histone modifications that are not bound by PML-RARα. Each dot identifies one promoter or CpG island. Data are based on the promoter arrays except the plots involving HDAC1 binding, which are based on the CpG island arrays. All axes indicate the difference between zinc-induced PML-RARα–expressing cells (Pr9) versus control cells (PMT). The indicated correlation coefficients are all significant at the P value less than .001 level, with the exception of r = −.18 (P = .03) for the association between trimethylation of lysine 9 and histone H3 acetylation for PML-RARα–bound genes. (A) Association between trimethylation of H3 lysine 4 and dimethylation of H3 lysine 4. Quadrant i shows an increase in trimethylation and a decrease in dimethylation of histone H3 lysine 4 for PML-RARα bound promoters. (B) Association between H3 lysine 9 trimethylation and H3 acetylation. Quadrant iv indicates a decrease in H3 acetylation and an increase in H3 lysine 9 methylation in most direct PML-RARα target genes (right panel), but not in promoters that are not targeted by PML-RARα (left panel). (C) Association between H3 acetylation and HDAC1 binding. Quadrant iv shows an decrease in H3 acetylation and an increase in HDAC1 binding.