Histone deacetylase. Association with a nuclease resistant, high molecular weight fraction of HeLa cell chromatin.

The chromatin-bound histone deacetylase of HeLa cells has been studied using endogenous [3H]acetyl-labeled polynucleosomes containing the enzyme, prepared in the presence of 40 mM butyrate. Histone deacetylase was assayed upon removal of the butyrate, and it was found that active enzyme is found only in association with a high molecular weight complex. This deacetylase-containing complex is relatively resistant to digestion with micrococcal nuclease. No activity is found on mononucleosomes or oligonucleosomes. Up to 90% of labeled acetyl groups are removed from histone deacetylase complexes incubated in the absence of butyrate. Free histones are a poor substrate under these conditions, but histones in mononucleosomes are deacetylated when they are incubated with histone deacetylase complex. Histone deacetylase remains bound to this complex in 1-2 M NaCl and does not dissociate from it during its reaction with acetylated core histones. Under typical nuclease digestion conditions, the histone deacetylase complex contains DNA with a size distribution of 5-11 kilobase pairs and a variety of nonhistone proteins. Comparison of the protein composition of histone deacetylase complexes with that of nuclear matrix preparations shows some similarities. Taken together, the results on the chromatographic behavior, the DNA fragment sizes, and the protein composition of the deacetylase complex suggest that protein-protein interactions may be important in maintaining its structure and also in the binding of the deacetylase itself to the complex.