title: From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: nanoscale modeling of the nucleosomal stem.
abstract: The interaction of histone H1 with linker DNA results in the formation of the nucleosomal stem structure, with considerable influence on chromatin organization. In a recent paper [Syed,S.H., Goutte-Gattat,D., Becker,N., Meyer,S., Shukla,M.S., Hayes,J.J., Everaers,R., Angelov,D., Bednar,J. and Dimitrov,S. (2010) Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome. Proc. Natl Acad. Sci. USA, 107, 9620-9625], we published results of biochemical footprinting and cryo-electron-micrographs of reconstituted mono-, di- and tri-nucleosomes, for H1 variants with different lengths of the cationic C-terminus. Here, we present a detailed account of the analysis of the experimental data and we include thermal fluctuations into our nano-scale model of the stem structure. By combining (i) crystal and NMR structures of the nucleosome core particle and H1, (ii) the known nano-scale structure and elasticity of DNA, (iii) footprinting information on the location of protected sites on the DNA backbone and (iv) cryo-electron micrographs of reconstituted tri-nucleosomes, we arrive at a description of a polymorphic, hierarchically organized stem with a typical length of 20 ± 2 base pairs. A comparison to linker conformations inferred for poly-601 fibers with different linker lengths suggests, that intra-stem interactions stabilize and facilitate the formation of dense chromatin fibers.
authors.affiliation: Laboratoire de Physique and Centre Blaise Pascal, École Normale Supérieure de Lyon, Université de Lyon, CNRS UMR 5672, 46 allée d'Italie 69364 Lyon cedex 07, France. sam.meyer@ens-lyon.fr
authors.forename: Sam
authors.initials: S
authors.lastname: Meyer
authors.forename: Nils B
authors.initials: NB
authors.lastname: Becker
authors.forename: Sajad Hussain
authors.initials: SH
authors.lastname: Syed
authors.forename: Damien
authors.initials: D
authors.lastname: Goutte-Gattat
authors.forename: Manu Shubhdarshan
authors.initials: MS
authors.lastname: Shukla
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Hayes
authors.forename: Dimitar
authors.initials: D
authors.lastname: Angelov
authors.forename: Jan
authors.initials: J
authors.lastname: Bednar
authors.forename: Stefan
authors.initials: S
authors.lastname: Dimitrov
authors.forename: Ralf
authors.initials: R
authors.lastname: Everaers
mesh_terms: D001696:Biomechanical Phenomena; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D006657:Histones / Q000737:chemistry; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009707:Nucleosomes / Q000737:chemistry*; D023302:Protein Footprinting
chemical_list: D006657:Histones; D009707:Nucleosomes; D004247:DNA