Evidence for nucleosome depletion at active regulatory regions genome-wide

yeast. Whether such remodeling is a general feature of gene regulation that operates across the yeast genome is not known. We therefore sought to determine relative nucleosome occupancy throughout the genome. We prepared extracts from yeast cells in which the only source of histone H4 was tagged with the Myc epitope and carried out chromatin immunoprecipitation (ChIP) assays using antibodies to Myc. To assess the relative abundance of genomic fragments enriched by ChIP, we treated samples with RNase, amplified them and labeled them fluorescently. In parallel, we prepared total genomic DNA from input extract, amplified it and labeled it with a different fluorescent marker. We then analyzed the two samples by comparative hybridization to DNA microarrays that cover the entire yeast genome at a resolution of ∼1 kb. The ChIPs of Myc-tagged histone H4 enriched DNA