From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: nanoscale modeling of the nucleosomal stem.

Sam Meyer (1) , Nils B Becker , Sajad Hussain Syed (2) , Damien Goutte-Gattat (2) , Manu Shubhdarshan Shukla (2) , Jeffrey J Hayes , Dimitar Angelov (3) , Jan Bednar (4) , Stefan Dimitrov (2) , Ralf Everaers

1 Phys-ENS - Laboratoire de Physique de l'ENS Lyon
2 INSERM U823 - Institut d'oncologie/développement Albert Bonniot de Grenoble
3 LBMC - Laboratoire de Biologie Moléculaire de la Cellule
4 LSP - Laboratoire de Spectrométrie Physique

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.

Mots clés: CHROMATIN FIBER STRUCTURE; LINKER HISTONE H5; CORE PARTICLE; ANGSTROM RESOLUTION; H4-K16 ACETYLATION; BINDING; REVEALS

Mots clés: GLOBULAR DOMAIN; MOLECULAR-DYNAMICS; DNA

Domaines: Biologie structurale [q-bio.BM]

Sam Meyer, Nils B Becker, Sajad Hussain Syed, Damien Goutte-Gattat, Manu Shubhdarshan Shukla, et al.. From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: nanoscale modeling of the nucleosomal stem.. Nucleic Acids Research, 2011, 39 (21), pp.9139-54. ⟨10.1093/nar/gkr573⟩. ⟨hal-00726331⟩