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Sir2p exists in two nucleosome‐binding complexes with distinct deacetylase activities

The absolute requirement for the histone deacetylase activity of Sir2p in silencing coupled with the conservation of Sir2p‐like proteins in larger eukaryotes suggests that this molecule plays an important role in gene regulation in all organisms. Here we report the purification and characterization of two Sir2p‐containing protein complexes; one of which contains Sir4p and the other Net1p. The Sir4p‐containing complex has an NAD‐dependent histone deacetylase activity, while the Net1p‐containing complex possesses deacetylase activity but only weak NAD‐dependent histone deacetylase activity. Finally, we demonstrate that the Sir2p‐containing complexes bind nucleosomes efficiently and partially restrict accessibility of the linker DNA to enzymatic probes.