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

Sam Meyer, Nils B. Becker, Sajad Hussain Syed, Damien Goutte-Gattat, Manu Shubhdarshan Shukla, Jeffrey J. Hayes, Dimitar Angelov, Jan Bednar, Stefan Dimitrov, Ralf Everaers

Research output: Contribution to journalArticle

30 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)9139-9154
Number of pages16
JournalNucleic Acids Research
Volume39
Issue number21
DOIs
Publication statusPublished - Nov 2011
Externally publishedYes

Fingerprint

Nucleosomes
Electrons
Chromatin
DNA Footprinting
DNA
Elasticity
Base Pairing
Histones
Hot Temperature

ASJC Scopus subject areas

  • Genetics

Cite this

Meyer, S., Becker, N. B., Syed, S. H., Goutte-Gattat, D., Shukla, M. S., Hayes, J. J., ... Everaers, R. (2011). From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: Nanoscale modeling of the nucleosomal stem. Nucleic Acids Research, 39(21), 9139-9154. https://doi.org/10.1093/nar/gkr573

From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures : Nanoscale modeling of the nucleosomal stem. / Meyer, Sam; Becker, Nils B.; Syed, Sajad Hussain; Goutte-Gattat, Damien; Shukla, Manu Shubhdarshan; Hayes, Jeffrey J.; Angelov, Dimitar; Bednar, Jan; Dimitrov, Stefan; Everaers, Ralf.

In: Nucleic Acids Research, Vol. 39, No. 21, 11.2011, p. 9139-9154.

Research output: Contribution to journalArticle

Meyer, S, Becker, NB, Syed, SH, Goutte-Gattat, D, Shukla, MS, Hayes, JJ, Angelov, D, Bednar, J, Dimitrov, S & Everaers, R 2011, 'From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: Nanoscale modeling of the nucleosomal stem', Nucleic Acids Research, vol. 39, no. 21, pp. 9139-9154. https://doi.org/10.1093/nar/gkr573
Meyer, Sam ; Becker, Nils B. ; Syed, Sajad Hussain ; Goutte-Gattat, Damien ; Shukla, Manu Shubhdarshan ; Hayes, Jeffrey J. ; Angelov, Dimitar ; Bednar, Jan ; Dimitrov, Stefan ; Everaers, Ralf. / From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures : Nanoscale modeling of the nucleosomal stem. In: Nucleic Acids Research. 2011 ; Vol. 39, No. 21. pp. 9139-9154.
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