Histones are the predominant protein components of chromatin and are subject to a variety of specific post-translational modifications that are correlated with transcriptional competence. Among these modifications are reversible acetylation that is mediated by acetyltransferases that mediate transcriptional activation and deactylases that mediate transcriptional repression and gene silencing. Structural studies have provided important insights into the mechanism of substrate specific binding and catalysis by the enzymes that mediate reversible acetylation. In this paper I will review structural work from my laboratory on histone acetyltransferases (HATs) and the Sir2 family of histone deacetylases (HDACs), with a specific focus on catalysis and substrate-specific binding by these enzymes.