Transcriptional silencing is a gene control mechanism resulting in epigenetic repression of large (>1 gene) chromosomal domains. This type of treanscriptional repression - which occurs near telomeres, in the nucleolar rDNA, and at the silent mating type loci of yeast - is correlated with significant changes in chromatin structure that are thought to limit the accessibility of the silenced chromosomal domains to transcriptional machinery. At least two types of proteins are intimately associated with silent chromatin in the yeast, Saccharomyces cerevisiae: Sir (silent information regulator) proteins and the core histones. The Sir2 protein is required for all forms of silencing, while Sir3 and Sir4 are required for telomeric and HM loci silencing only. Sir proteins are specifically associated with silent chromatin, although their precise roles in silencing remain to be elucidated. The N-terminal tails of histones H3 and H4, which are required for silencing at the silent mating type (HM) loci and at telomeres, are known to bind Sir3p and Sir4p. We and others have recently shown that Sir2p and its homologs are potent NAD-dependent protein deacetylases, whose substrates include the N-terminal tails of histones. While this observation has opened up a wealth of new possibilities regarding how genes are silenced, the underlying mechanisms are poorly understood. We will use the tools of molecular genetics, biochemistry and structural biology to carry out a comprehensive analysis of the molecular mechanisms involved in silencing.
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