title: Nucleosome repositioning underlies dynamic gene expression.
abstract: Nucleosome repositioning at gene promoters is a fundamental aspect of the regulation of gene expression. However, the extent to which nucleosome repositioning is used within eukaryotic genomes is poorly understood. Here we report a comprehensive analysis of nucleosome positions as budding yeast transit through an ultradian cycle in which expression of >50% of all genes is highly synchronized. We present evidence of extensive nucleosome repositioning at thousands of gene promoters as genes are activated and repressed. During activation, nucleosomes are relocated to allow sites of general transcription factor binding and transcription initiation to become accessible. The extent of nucleosome shifting is closely related to the dynamic range of gene transcription and generally related to DNA sequence properties and use of the coactivators TFIID or SAGA. However, dynamic gene expression is not limited to SAGA-regulated promoters and is an inherent feature of most genes. While nucleosome repositioning occurs pervasively, we found that a class of genes required for growth experience acute nucleosome shifting as cells enter the cell cycle. Significantly, our data identify that the ATP-dependent chromatin-remodeling enzyme Snf2 plays a fundamental role in nucleosome repositioning and the expression of growth genes. We also reveal that nucleosome organization changes extensively in concert with phases of the cell cycle, with large, regularly spaced nucleosome arrays being established in mitosis. Collectively, our data and analysis provide a framework for understanding nucleosome dynamics in relation to fundamental DNA-dependent transactions.
authors.affiliation: Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; BCMB Graduate Program, Weill Cornell Medical College, New York, New York 10065, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Nocetti
authors.affiliation: Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
authors.forename: Iestyn
authors.initials: I
authors.lastname: Whitehouse
mesh_terms: D001483:Base Sequence / Q000235:genetics; D002843:Chromatin / Q000737:chemistry; D042002:Chromatin Assembly and Disassembly / Q000235:genetics; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D006657:Histones / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D006657:Histones; C493530:Htz1 protein, S cerevisiae; D009707:Nucleosomes; C445179:SWI-SNF-B chromatin-remodeling complex; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors
keywords: SWI/SNF; chromatin; nucleosome; transcription