Abstract
A genome-wide study of nucleosome occupancy at yeast promoters shows that promoters that regulate active genes, contain multiple conserved motifs, or contain Rap1 binding sites tend to be depleted of nucleosomes.
Highlights
Eukaryotic genomes are generally thought to be entirely chromatinassociated, the activated PHO5 promoter in yeast is largely devoid of nucleosomes
We suggest that other transcription factors have less robust nucleosome-depleting activities than Rap1 and must act collaboratively to gain access to their cognate sites in the DNA
We found that regions depleted in the H3 chromatin immunoprecipitation (ChIP) assay overlap extensively with regions enriched by aqueous extraction, but not with regions depleted by aqueous extraction (Figure 1d)
Summary
Eukaryotic genomes are generally thought to be entirely chromatinassociated, the activated PHO5 promoter in yeast is largely devoid of nucleosomes. We systematically evaluated nucleosome occupancy in yeast promoters by immunoprecipitating nucleosomal DNA and quantifying enrichment by microarrays. Global gene-expression patterns are established and maintained by the concerted actions of transcription factors and the proteins that constitute chromatin. The global network of interactions between transcription factors and promoters in yeast is increasingly being characterized [1]. The distribution of nucleosomes, the fundamental units of chromatin, is poorly understood on a gene-specific basis, much less a global basis [2]. The nucleosome consists of approximately 146 base-pairs (bp) of DNA wrapped around an octamer of histone proteins - two each of histones H2A, H2B, H3 and H4.
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