Investigating the Acute Effects of Histone Deacetylase 1 Degradation in Mouse Embryonic Stem Cells

Histone deacetylase (HDACs) enzymes remove acetyl-moieties from post-translationally modified lysine residues on histones, resulting in chromatin compaction and gene silencing. The Class I HDACs, HDAC1 and HDAC2, are well-characterised and are largely redundant. Genetic ablation experiments have, however, shown that HDAC1 is uniquely required in early mouse embryonic development since deletion of Hdac1 but not Hdac2 is lethal by embryonic day 10.5. Although current genetic manipulation techniques have provided some answers, they are limited by slow depletion rates and downstream effects diluting the primary impacts of HDAC1-degradation. Herein, the degradation tag (dTAG) system has been leveraged to achieve rapid (within 2 hours) degradation of HDAC1 enabling the immediate effects of HDAC1 removal to be investigated.As anticipated, HDAC1 degradation resulted predominantly in the upregulation of transcription within 2 hours, with progressive increases in downregulated genes over time. In particular, pluripotency-associated factors and ribosome biogenesis genes were downregulated, while circadian rhythm and nervous system development genes were upregulated within 2 and 6 hours of HDAC1 depletion. ATAC-seq demonstrated that dysregulated gene expression was accompanied by widespread alterations in chromatin accessibility, with an unexpected gradual loss of accessibility at super-enhancers (SEs), correlating with a reduction in the expression of SE-dependent genes. Using the dTAG system, this study has both reinforced HDAC1’s role as a chromatin repressor and has also provided novel insights into the immediate regulatory dynamics of HDAC1, uncovering complexities that were previously obscured in genetic knockout and inhibitor-based studies.