Sir proteins impede, but do not prevent, access to silent chromatin in living Saccharomyces cerevisiae.

Gene silencing at the mating-type loci in budding yeast (HMRa and HMLα) depends on the Sir proteins. Sir2, Sir3 and Sir4 are indispensable, whereas Sir1 has a limited role. Sir proteins are also involved in repression at telomeres and rDNA repeats. Sir proteins may mediate silencing by limiting access to DNA. Using an inducible DNA methyltransferase expression system, we showed previously that the silenced mating-type loci are methylated at a much slower rate than the rest of the genome in vivo. Here, we show that Sir2, Sir3 and Sir4 are all required to impede access to the mating-type loci and telomeric X-elements. rDNA access is impeded by Sir2 and Sir3, but not Sir4. Methylation rates at adjacent rDNA repeats are not strongly correlated, suggesting that Sir proteins silence rDNA repeats randomly. Sir1 is required to impede access to HMRa, but not to HMLα, telomeres or rDNA. Since silenced DNA is accessible in vivo, albeit at a slower rate than elsewhere in the genome, steric occlusion is unlikely to be the primary mechanism of silencing.