title: Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations.
abstract: It has been shown experimentally that the action of the RSC chromatin remodeler leads to the formation of an irregular, partially remodeled nucleosome, termed a remosome. The remosome contains an extra 30-40 base pairs of DNA compared to a canonical nucleosome. Large-scale molecular simulations have provided information on the probable structure of remosomes and have explained why they remain stable in the absence of RSC. Here we explain how these simulations were carried out and what the resulting remosome models imply in terms of the mechanism of action of RSC. We notably show that local kinks within DNA are key in explaining how extra DNA can be in added to nucleosomes without unduly disturbing DNA-histone binding.
authors.affiliation: a Université de Lyon/CNRS UMR 5086, MMSB, Institut de Biologie et Chimie des Protéines , Lyon , France.
authors.forename: Marco
authors.initials: M
authors.lastname: Pasi
authors.affiliation: b Université de Lyon/CNRS/INRA UMR 5239, LBMC, Ecole Normale Supérieure de Lyon , Lyon , France.
authors.forename: Dimitar
authors.initials: D
authors.lastname: Angelov
authors.affiliation: c Institut Albert Bonniot, Université de Grenoble Alpes/INSERM U1209/CNRS UMR 5309 , Grenoble , France.
authors.forename: Jan
authors.initials: J
authors.lastname: Bednar
authors.affiliation: c Institut Albert Bonniot, Université de Grenoble Alpes/INSERM U1209/CNRS UMR 5309 , Grenoble , France.
authors.forename: Stefan
authors.initials: S
authors.lastname: Dimitrov
authors.affiliation: a Université de Lyon/CNRS UMR 5086, MMSB, Institut de Biologie et Chimie des Protéines , Lyon , France.
authors.forename: Richard
authors.initials: R
authors.lastname: Lavery
mesh_terms: D004247:DNA / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D009707:Nucleosomes; D004247:DNA
keywords: DNA; DNA kinks; DNA loops; RSC; SWI/SNF; chromatin remodeling; molecular dynamics; nucleosome; remosome