Histone and non-histone protein acetylation in a tail regeneration model (Ambystoma mexicanum)

Histone deacetylase inhibitors (HDACi) potently inhibit appendage regeneration, but how HDACi alter protein acetylation is relatively unexplored. Using genomic, transcriptomic, and proteomic approaches, we report HDACi-mediated changes in gene expression and protein acetylation at the outset of Ambystoma mexicanum tail regeneration. HDACi (romidepsin) treatment globally reversed a genome-wide deacetylation response after tail amputation, broadly increasing H3K9ac and H3K27ac within intergenic regions, gene promoters, and gene bodies. Changes in promoter acetylation were only weakly associated with changes in gene expression when considering all acetylated genes. However, the magnitude of acetylation change was significantly greater for upregulated genes, including previously identified regeneration-inhibitory genes. We further detected hundreds of differentially acetylated non-histone proteins after tail amputation, including proteins that function in transcriptional regulation and hemostasis. We used a small molecule (A-485) to inhibit differentially acetylated transcription factors (Crebbp/Ep300) to show their requirement for tail regeneration. A-485 downregulated many of the same genes that were downregulated by romidepsin, but the upregulated gene set was relatively unique. Our results implicated histone and non-histone protein acetylation in the early transcriptional regulation of regeneration associated genes.