Modulation of transcription of active vs inactive genes by HDACi. (A) Comparison in erythroid cells of basal mRNA expression levels of groups of genes modulated (up- and downregulated, all genes together or as individual groups) with genes that show no change in response to HDACi. The basal expression level of all genes (All) is also shown. Genes were ranked according to a cutoff of 1.5-fold change and P < .05. (B) The same analysis as in (A) of the GSE15735 data set. CD4⁺ T cells were treated with 100 ng/mL TSA and 2 mM NaBu for 12 hours. Box blots show 25% to 75% quartiles; horizontal lines show the mean, and whiskers show the 10th to 90th percentiles. One-way analysis of variance (ANOVA) corrected for multiple comparisons; ****P < .0001. (C) De novo motif identification in the promoters of the 70 most up- vs downregulated and most upregulated vs no change genes after NaBu treatment. A GC-rich motif (Motif A) was the most highly enriched in the promoters of the upregulated genes in both group comparisons. In downstream analysis, Motif A was identified as an Sp1 binding site (supplemental Figure 2A).