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Single-base resolution mapping of H1–nucleosome interactions and 3D organization of the nucleosome

Sajad Hussain Syed1,2, Damien Goutte-Gattat1, Nils Becker3, Sam Meyer3, Manu Shubhdarshan Shukla1,2, Jeffrey J. Hayes4, Ralf Everaers3, Dimitar Angelov2, Jan Bednar5,6,a, and Stefan Dimitrov1,b

1Inserm U823, Université Joseph Fourier – Grenoble 1, Institut Albert Bonniot, Site Santé BP 170, 38042 Grenoble cedex 9, France

2Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS UMR 5239, École Normale Supérieure de Lyon, 46 allée d’Italie, 69007 Lyon, France

3Laboratoire de Physique et Centre Blaise Pascal, École Normale Supérieure de Lyon, CNRS UMR 5672, Université de Lyon, 46 allée d’Italie, 69634 Lyon cedex 7, France

4Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester NY 14642

5Laboratoire de Spectrométrie Physique, CNRS/UJF UMR 5588, BP 87, 140 avenue de la physique, 38042 St-Martin d’Hères, France

6Charles University in Prague, First Faculty of Medicine, Institute of Cellular Biology and Pathology and Department of Cell Biology, Institute of Physiology, Academy of Sciences of the Czech Republic, Albertov 4, 128 01 Prague 2, Czech Republic

aCorresponding author:

bCorresponding author:

This work was published in the Proceedings of the National Academy of Sciences of the United States of America (PNAS). As one of the authors, I reproduce it here as I am entitled to do according to the PNAS License to Publish.

Proc. Natl. Acad. Sci. USA, 107(21):9620–9625. [full text]


Despite the key role of the linker histone H1 in chromatin structure and dynamics, its location and interactions with nucleosomal DNA have not been elucidated. In this work we have used a combination of electron cryomicroscopy, hydroxyl radical footprinting, and nanoscale modeling to analyze the structure of precisely positioned mono-, di-, and trinucleosomes containing physiologically assembled full-length histone H1 or truncated mutants of this proteins. Single-base resolution •OH footprinting shows that the globular domain of histone H1 (GH1) interacts with the DNA minor groove located at the center of the nucleosome and contacts a 10-bp region of DNA localized symmetrically with respect to the nucleosomal dyad. In addition, GH1 interacts with and organize about one helical turn of DNA in each linker region of the nucleosome. We also find that a seven amino acid residue region (121–127) in the COOH terminus of histone H1 was required for the formation of the stem structure of the linker DNA. A molecular model on the basis of these data and coarse-grain DNA mechanics provides novel insights on how the different domains of H1 interact with the nucleosome and predicts a specific H1-mediated stem structure within linker DNA.

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pnas-107-21-9620.pdf (application/pdf, 2.4M)