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

Sam Meyer1,a, Nils B. Becker1,2, Sajad Hussain Syed3,4, Damien Goutte-Gattat3, Manu Shubhdarshan Shukla3,4, Jeffrey J. Hayes5, Dimitar Angelov4, Jan Bednar6,7,8, Stefan Dimitrov3, and Ralf Everaers1

1Laboratoire de Physique and Centre Blaise Pascal, École Normale Supérieure de Lyon, Université de Lyon, CNRS UMR 5672, 46 allée d’Italie, 69364 Lyon cedex 7, France

2FOM Institute AMOLF, Science park 104, 1098 XG Amsterdam, The Netherlands

3INSERM; Université Joseph Fourier – Grenoble 1, Institut Albert Bonniot, U823, France

4Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS UMR 5239/INRA 1237/UFR 128 Biosciences, France

5Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USA

6Univ. Grenoble 1/CNRS, LIPhy UMR 5588, Grenoble, F-38041, France

7Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology Albertov 4, 128 01 Prague 2, Czech Republic

8Department of Cell Biology, Institute of Physiology, Academy of Sciences of the Czech Republic, 128 01 Prague 2, Czech Republic

aCorresponding author:

This article was published in Nucleic Acids Research (NAR) under a Creative Commons Attribution Non-Commercial License.

Nucl. Acids Res., 39(21):9139–9154. [full text]


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 detailled 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 fiber.

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Here is the final published article:

nar-39-21-9139.pdf (application/pdf, 14M)