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 HML) depends on the Sir proteins. Sir2, Sir3 and Sir4 are indispensable for silencing, whereas Sir1 has a more limited role. The Sir proteins are also involved in repression at telomeres and ribosomal DNA (rDNA) repeats. Proposed mechanisms for Sir-mediated silencing include limiting access to silenced DNA and inhibition of transcript initiation and/or elongation. Using an inducible M.SssI 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, in the absence of Sir2, Sir3 or Sir4, the silenced loci and the telomeric X elements are methylated at a similar rate to the rest of the genome, indicating that these Sir proteins impede access, but do not prevent it. The rDNA repeats are methylated faster in the absence of Sir2 and, to a lesser extent, of Sir3, but not of Sir4. The methylation rates of adjacent rDNA repeats are not strongly correlated in wild-type cells, suggesting that Sir proteins silence rDNA repeats randomly. Loss of Sir1 increases the methylation rate at HMRa but not at HML, telomeres or rDNA. Our data indicate that steric occlusion is unlikely to be the primary mechanism of silencing, since silenced DNA is accessible in vivo, albeit at a slower rate than elsewhere in the genome.