title: A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern.
abstract: Although the genomic pattern of nucleosome positioning is broadly conserved, quantitative aspects vary over evolutionary timescales. We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. Strikingly, in a foreign species, nucleosome-depleted regions occur fortuitously in coding regions, and they often act as promoters that are associated with a positioned nucleosome array linked to the length of the transcription unit. We suggest a three-step model in which nucleosome remodelers, general transcription factors, and the transcriptional elongation machinery are primarily involved in generating the nucleosome positioning pattern in vivo.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,Worcester, MA 01605, USA.
authors.forename: Amanda L
authors.initials: AL
authors.lastname: Hughes
authors.forename: Yi
authors.initials: Y
authors.lastname: Jin
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Rando
authors.forename: Kevin
authors.initials: K
authors.lastname: Struhl
mesh_terms: D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly; D018244:Chromosomes, Artificial, Yeast / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D016681:Genome, Fungal; D008954:Models, Biological; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism*; D011067:Poly dA-dT / Q000235:genetics; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D061785:Transcription Initiation, Genetic
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D011067:Poly dA-dT