Vascular histone deacetylation by pharmacological HDAC inhibition

Biological effects of TSA in primary human vascular endothelial cells. (A) Genome-wide distribution of chromatin marks shows significant H3K9/14 acetylation and deacetylation by HDAC inhibition. The plots shown compare the number of tags (the log₂ of the read abundance, i.e., logConcentration determined by edgeR) versus the log₂ fold change (log₂FC). Regions subject to significant changes are shown in red (adjusted P < 0.05), and nonsignificant changes are shown in black for TSA-stimulated HAECs. Distribution plots were divided into four quadrants for H3K9/14ac and H3K4me3. (B) The number of differential H3K9/14ac regions (adjusted P < 0.05). Determination of differential enrichment is described in the Methods. (C) The percentage of differential H3K9/14ac regions (adjusted P < 0.05) located within the gene promoter (2.5 kb either side of the TSS). Enrichment of H3K9/14ac by genomic feature (D) and mRNA/ncRNA (E) was determined using Fisher’s exact test. The log₂ odds ratio for the genomic distribution of increased and decreased H3K9/14ac is represented. Error bars represent 95% confidence intervals.