Silencing of the HMR domain in Saccharomyces cerevisiae requires the action of a DNA element called a silencer that binds sequence-specific DNA binding proteins to form a silencer-protein complex (SPC). The SPC recruits specialized chromatin proteins, the Sir proteins that deacetylate and bind nucleosomes within HMR. Sir-dependent chromatin is absolutely necessary to repress transcription of a gene within HMR and causes repression at a step after recruitment of the RNA Pol II holoenzyme. Specific mechanisms that include specialized nucleosomes help confine Sir-dependent chromatin to HMR.