title: Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes.
abstract: We have used paired-end sequencing of yeast nucleosomal DNA to obtain accurate genomic maps of nucleosome positions and occupancies in control cells and cells treated with 3-aminotriazole (3AT), an inducer of the transcriptional activator Gcn4. In control cells, 3AT-inducible genes exhibit a series of distinct nucleosome occupancy peaks. However, the underlying position data reveal that each nucleosome peak actually consists of a cluster of mutually exclusive overlapping positions, usually including a dominant position. Thus, each nucleosome occupies one of several possible positions and consequently, different cells have distinct local chromatin structures. Induction results in a major disruption of nucleosome positioning, sometimes with altered spacing and a dramatic loss of occupancy over the entire gene, often extending into a neighbouring gene. Nucleosome-depleted regions are generally unaffected. Genes repressed by 3AT show the same changes, but in reverse. We propose that yeast genes exist in one of several alternative nucleosomal arrays, which are disrupted by activation. We conclude that activation results in gene-wide chromatin remodelling and that this remodelling can even extend into the chromatin of flanking genes.
authors: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Building 6A, Room 2A14, 6 Center Dr, 9000 Rockville Pike, Bethesda, Maryland 20892, USA.
authors: Hope A
authors: HA
authors: Cole
authors: Bruce H
authors: BH
authors: Howard
authors: David J
authors: DJ
authors: Clark
mesh_terms: D000135:Acid Phosphatase / Q000235:genetics; D019747:Aldose-Ketose Isomerases / Q000235:genetics; D000640:Amitrole / Q000494:pharmacology; D001119:Arginase / Q000235:genetics; D050976:Basic-Leucine Zipper Transcription Factors / Q000378:metabolism*; D002843:Chromatin / Q000737:chemistry; D042002:Chromatin Assembly and Disassembly; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D056426:Genetic Loci; D009707:Nucleosomes / Q000737:chemistry*; D011401:Promoter Regions, Genetic; D018741:Replication Origin; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D015533:Transcriptional Activation
chemical_list: D050976:Basic-Leucine Zipper Transcription Factors; D002843:Chromatin; C501391:GCN4 protein, S cerevisiae; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D000135:Acid Phosphatase; C488916:PHO5 protein, S cerevisiae; C540423:ARG1 protein, S cerevisiae; D001119:Arginase; D019747:Aldose-Ketose Isomerases; C490353:TRP1 protein, S cerevisiae; D000640:Amitrole