HDAC inhibition induces specific changes in the regulatory chromatin resulting in wide-spread changes in the transcriptome of CLL. (A) RNA seq was conducted in 10 CLL samples exposed to 0.4 μM abexinostat for 24 hours. Transcripts from cluster 1(HDAC1-BRD4-H3K27Ac-H3K9Ac-Pol2), cluster II (HDAC1-H3K9Ac-Pol2, or cluster III (HDAC only) or those with no marks were divided into high, intermediate, and low expressors. The y-axis shows the fold change (log2, with an FDR of 0.05) in counts of high-, medium-, and low-expressed transcripts after HDAC inhibition from cluster 1(HDAC1-BRD4-H3K27Ac-H3K9Ac-Pol2), cluster II (HDAC1-H3K9Ac-Pol2), or cluster III (HDAC only). Among high expressors, only genes from cluster I were downregulated, whereas intermediate expressors from cluster II and low expressors from cluster I to III were upregulated. Intermediate (∼20) and low expressors (∼55%) with no marks did not change expression after HDAC inhibition. (B) Expression of HDAC1 protein in 5 CLL samples after exposure to 0.4 μM abexinostat for 24 hours. GAPDH assayed as loading control. (C) The y-axis shows log2-fold changes in the occupancy of HDAC1, H3K9Ac, BRD4, H3K27Ac, and RNA Pol 2 near genes with high, intermediate, or low expression that became upregulated or downregulated twofold or more after HDAC inhibition. GAPDH, glyceraldehyde-3-phosphate dehydrogenase.