Nucleosome depletion in the vicinity of Rap1-binding sites. (a) Overlap between the 308 most nucleosome-depleted promoters and promoters found to recruit Rap1 in a global ChIP study . (b) Nucleosome depletion in the vicinity of Rap1-binding sites in ribosomal gene promoters evaluated by ChIP. Fold-enrichment was determined by real-time PCR using primers that span Rap1-binding motifs in the RPS22A, RPS15, RPS11B and RPL23A promoters. (c) Southern blots showing DNA from yeast spheroplasts digested with increasing concentrations of micrococcal nuclease probed with labeled PCR products spanning the TUB2 promoter and the Rap1 sites in the RPS11B and RPS15 promoters. (d) Nucleosome occupancy for a mutant RPS11B promoter lacking Rap1 consensus sites was determined by H3 ChIP and real-time PCR. The mutant promoter is enriched 2.1-fold relative to wild type. (e) Nucleosome occupancy at Rap1-binding sites in ribosomal protein gene promoters after treatment with rapamycin evaluated by H3 ChIP and real-time PCR.