Reversible modifications, such as acetylation or methylation, play a key role in defining chromatin states and in regulating transcription from genomic DNA differentially across distinct tissues. Several groups in the Chemical Biology Program study the enzymes that catalyze chromatin modifications using RNAi and chemical approaches. A primary focus of our chromatin research has been to illuminate the functions of individual members of the class-I and class-II histone deacetylases (HDACs) with the goal of understanding whether the functions are overlapping and redundant, redundant but dependent on temporal and spatial regulation of their expression, or unique to individual members. We use a variety of approaches, including direct binding assays, biochemical assays, and cellular assays, to identify compounds that serve as probes of function for chromatin modifying enzymes. For example, considerable effort is placed on the discovery of novel small-molecule modulators of HDACs that specifically target individual family members or that target functions distinct from enzymatic activities, such as protein-protein interactions involving cofactors or other members of the transcriptional machinery. There is also a considerable effort to identify small molecules that regulate the methylation of chromatin by targeting histone methyltransferases (HMTs) or histone demethylases (HDMs). Insights from these screening efforts feedback into the design and synthesis of chromatin-biased compound libraries including “biasing elements” that provide affinity for HDACs, HMTs, and HDMs. Finally, efforts are underway to identify chromatin-targeting compounds that alter the amounts of mRNA encoding therapeutic proteins, thereby altering the levels of protein. This research may provide an alternative path toward chromatin-based therapeutics.