High-resolution structural analysis of chromatin at specific loci:: Saccharomyces cerevisiae silent mating type locus HMLα

Genetic studies have suggested that chromatin structure is involved in repression of the silent mating type loci in Saccharomyces cerevisiae. Chromatin mapping at nucleotide resolution of the transcriptionally silent HML alpha and the active MAT alpha shows that unique organized chromatin structure characterizes the silent state of HML alpha. Precisely positioned nucleosomes abutting the silencers extend over the alpha 1 and alpha 2 coding regions. The HO endonuclease recognition site, nuclease hypersensitive at MAT alpha, is protected at HML alpha. Although two precisely positioned nucleosomes incorporate transcription start sites at HML alpha, the promoter region of the alpha 1 and alpha 2 genes is nucleosome free and more nuclease sensitive in the repressed than in the transcribed locus. Mutations in genes essential for HML silencing disrupt the nucleosome array near HML-I but not in the vicinity of HML-E, which is closer to the telomere of chromosome III. At the promoter and the HO site, the structure of HML alpha in Sir protein and histone H4 N-terminal deletion mutants is identical to that of the transcriptionally active MAT alpha. The discontinuous chromatin structure of HML alpha contrasts with the continuous array of nucleosomes found at repressed a-cell-specific genes and the recombination enhancer. Punctuation at HML alpha may be necessary for higher-order structure or karyoskeleton interactions. The unique chromatin architecture of HML alpha may relate to the combined requirements of transcriptional repression and recombinational competence.