PML-RARα–associated gene expression changes and regulated molecular functions. (A-C) Depiction of global alterations in mRNA expression with regard to PML-RARα binding or alterations in histone H3 acetylation or H3K9 trimethylation. The mRNA expression changes were analyzed by Affymetrix mRNA expression arrays (GeneChip HG-U133A) in 12-hour zinc-induced U937-PML-RARα cells versus U937–empty vector cells. (A) PML-RARα binding is associated with a significant decrease in mRNA expression levels. (B) Genes with increased histone H3 acetylation show increased gene expression and vice versa. (C) Increases in histone H3 lysine 9 trimethylation are associated with transcriptional repression. The boxes indicate the range of 50% of the data points and the whiskers contain 75% of the of the observed data points. (D) Analysis of the molecular functions of PML-RARα target genes. Significantly regulated genes for genomic PML-RARα binding, mRNA expression changes in PML-RARα–expressing U937 cells, and mRNA expression changes in PML-RARα–expressing murine promyelocytes (dataset kindly provided by Dr T. J. Ley) were analyzed for their association with molecular functions using Ingenuity IPA software 3.0. Molecular functions with significant (P < .05) enrichment in each of the 3 datasets are indicated.