Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [ATAC-seq]

Histone Deacetylase 1 (HDAC1) removes acetyl groups from lysine residues on the core histones, balancing histone acetyltransferase (HAT) activity. Despite this apparent repressive function, suppression of HDAC activity causes both up and downregulation of gene expression. Here we exploit the degradation tag (dTAG) system to rapidly degrade HDAC1 in embryonic stem cells (ESCs) lacking the paralog, HDAC2. Unlike HDAC inhibitors that lack isoform specificity the dTAG system allowed specific HDAC1 targeting and completely removed HDAC1 100x faster than genetic knockouts. HDAC1 degradation caused rapid increases in histone acetylation, with H2BK5 and H2BK11 most sensitive. The majority of differentially expressed genes following 2 hours of HDAC1 degradation were upregulated (275 genes up vs 15 down) with increased proportions of downregulated genes at 6 (1153 up vs 443 down) and 24 hours (1146 up vs 967 down). Upregulated genes showed increased H2BK5ac and H3K27ac around their transcriptional start site (TSS). In contrast, decreased acetylation of super-enhancers (SEs) was linked to the most strongly downregulated genes, leading to a collapse of the core pluripotency-associated gene network. These findings suggest that HDAC1 plays a crucial role in regulating the ESC gene expression network by maintaining the correct acetylation levels at key genomic sites. To investigate the consequences of HDAC1 removal in mouse embryonic stem cells we stably expressed a HDAC1-FKBP12F36V-Flag construct in conditional Hdac1/2 double knockout ESCs so that we could degrade the HDAC1-FKBP12F36V-Flag protein in the absence of endogenous HDAC1/2 and assay the consequences. We performed ATAC-seq following 2, 6 or 24 hours of HDAC1-FKBP12F36V-Flag degradation against a control treated with DMSO for 24 hours. Analysis allowed determination of genomic sites that show changes in accessibility following the degradation of HDAC1-FKBP12F36V.