title: Nucleosome positioning by genomic excluding-energy barriers.
abstract: Recent genome-wide nucleosome mappings along with bioinformatics studies have confirmed that the DNA sequence plays a more important role in the collective organization of nucleosomes in vivo than previously thought. Yet in living cells, this organization also results from the action of various external factors like DNA-binding proteins and chromatin remodelers. To decipher the code for intrinsic chromatin organization, there is thus a need for in vitro experiments to bridge the gap between computational models of nucleosome sequence preferences and in vivo nucleosome occupancy data. Here we combine atomic force microscopy in liquid and theoretical modeling to demonstrate that a major sequence signaling in vivo are high-energy barriers that locally inhibit nucleosome formation rather than favorable positioning motifs. We show that these genomic excluding-energy barriers condition the collective assembly of neighboring nucleosomes consistently with equilibrium statistical ordering principles. The analysis of two gene promoter regions in Saccharomyces cerevisiae and the human genome indicates that these genomic barriers direct the intrinsic nucleosome occupancy of regulatory sites, thereby contributing to gene expression regulation.
authors.affiliation: Universitè Claude Bernard Lyon 1, Université de Lyon, F-69000 Lyon, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Milani
authors.forename: Guillaume
authors.initials: G
authors.lastname: Chevereau
authors.forename: Cédric
authors.initials: C
authors.lastname: Vaillant
authors.forename: Benjamin
authors.initials: B
authors.lastname: Audit
authors.forename: Zofia
authors.initials: Z
authors.lastname: Haftek-Terreau
authors.forename: Monique
authors.initials: M
authors.lastname: Marilley
authors.forename: Philippe
authors.initials: P
authors.lastname: Bouvet
authors.forename: Françoise
authors.initials: F
authors.lastname: Argoul
authors.forename: Alain
authors.initials: A
authors.lastname: Arneodo
mesh_terms: D055592:Biophysical Phenomena; D015825:Chromosomes, Fungal / Q000737:chemistry / Q000235:genetics / Q000648:ultrastructure; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000648:ultrastructure; D023281:Genomics; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics* / Q000648:ultrastructure*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics / Q000648:ultrastructure; D013816:Thermodynamics
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes; D004247:DNA