SIR repression of a yeast heat shock gene: UAS and TATA footprints persistwithin heterochromatin

Previous work has suggested that products of the Saccharomyces cerevisiae S ilent Information Regulator (SIR) genes form a complex with histones, nucle ated by cis-acting silencers or telomeres, which represses transcription in a position-dependent but sequence-independent fashion. While it is general ly thought that this Sir complex works through the establishment of heteroc hromatin, it is unclear how this structure blocks transcription while remai ning fully permissive to other genetic processes such as recombination or i ntegration. Here we examine the molecular determinants underlying the silen cing of HSP82, a transcriptionally potent, stress-inducible gene. We find t hat HSP82 is efficiently silenced in a SIR-dependent fashion, but only when HMRE mating-type silencers are configured both 5' and 3' of the gene. Acco mpanying dominant repression are novel wrapped chromatin structures within both core and upstream promoter regions. Strikingly, DNase I footprints map ping to the binding sites for heat shock factor (HSF) and TATA-binding prot ein (TBP) are strengthened and broadened, while groove-specific interaction s, as detected by dimethyl sulfate, are diminished. Our data are consistent with a model for SIR repression whereby transcriptional activators gain ac cess to their cognate sites but are rendered unproductive by a co-existing heterochromatic complex.