Histone deacetylases (HDACs) are members of a diverse family of enzymes that catalyze the removal of an acetyl moiety from an acetyl-lysine-containing substrate. HDACs target a variety of substrates, including histone and nonhistone proteins, to mediate alterations in protein localization, stability, and activity. In addition, HDACs have been shown to modulate changes in gene expression, primarily through the recruitment of transcriptional cofactors to promoter regions. Mammalian HDACs are organized into distinct classes based on their homology to yeast HDACs. Classes I, II and IV HDACs are structurally and catalytically similar, whereas, class III HDACs require NAD(+) as a cofactor in the deacetylation reaction. This unit provides guidance for choosing and preparing a substrate suitable for assaying an HDAC of interest and describes key protocols necessary for assaying HDAC activity.
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