Nucleosome depletion in the vicinity of Rap1-binding sites

Copyright information:Taken from "Global nucleosome occupancy in yeast"Genome Biology 2004;5(9):R62-R62.Published online 20 Aug 2004PMCID:PMC522869.Copyright © 2004 Bernstein et al.; licensee BioMed Central Ltd. Overlap between the 308 most nucleosome-depleted promoters and promoters found to recruit Rap1 in a global ChIP study [1]. 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 , , and promoters. Southern blots showing DNA from yeast spheroplasts digested with increasing concentrations of micrococcal nuclease probed with labeled PCR products spanning the promoter and the Rap1 sites in the and promoters. Nucleosome occupancy for a mutant 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. Nucleosome occupancy at Rap1-binding sites in ribosomal protein gene promoters after treatment with rapamycin evaluated by H3 ChIP and real-time PCR.