Experimental strategies for evaluating the impact of HDACs and HDAC inhibitors on the epigenome. ChiP-seq

HDACs (histone deacetylases) are components of multiprotein complexes that remove the acetyl group from lysine residues (and other acyl groups) to regulate protein function. This important post-translational modification can affect the local hydrophobic environment of a specific protein surface. When the protein substrates are histones, the regulation of lysine acetylation influences chromatin accessibility and gene expression. Defining the different genomic regions under the influence of specific HDACs is fundamental to understanding how these enzymes control the epigenetic status of cells. Furthermore, it is important to clarify the mechanisms of action of HDAC inhibitors from a therapeutic perspective. ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) is a powerful technique to identify where histone acetylations regulated by HDACs or influenced by HDAC inhibitors occur in the genome. Here, we describe a protocol to perform a ChIP-seq experiment to detect the genome-wide distribution of histone acetylation.