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Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber

Abstract

The compaction of eukaryotic DNA into chromatin has been implicated in the regulation of all DNA processes. To unravel the higher-order folding of chromatin, we used magnetic tweezers and probed the mechanical properties of single 197-bp repeat length arrays of 25 nucleosomes. At forces up to 4 pN, the 30-nm fiber stretches like a Hookian spring, resulting in a three-fold extension. Together with a high nucleosome-nucleosome stacking energy, this points to a solenoid as the underlying topology of the 30-nm fiber. Unexpectedly, linker histones do not affect the length or stiffness of the fiber but stabilize its folding. Fibers with a nucleosome repeat length of 167 bp are stiffer, consistent with a two-start helical arrangement. The observed high compliance causes extensive thermal breathing, which forms a physical basis for the balance between DNA condensation and accessibility.

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Figure 1: Characterization of reconstituted chromatin fibers.
Figure 2: Force spectroscopy on chromatin fibers.
Figure 3: Chromatin fibers stretch like a Hookian spring, independently of the presence of linker histones.
Figure 4: Schematic representations of chromatin fiber conformations at different forces.
Figure 5: Depletion of Mg2+ destabilizes nucleosome stacking.
Figure 6: Increased length and stiffness of 167 NRL fibers.

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Acknowledgements

We would like to thank T. Richmond, H. Schiessel, T. Schmidt and J. Widom for helpful discussions. This work was financially supported by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek and the European Science Foundation.

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Contributions

C.L., D.R. and J.v.N. designed the research; F.T.C. performed experiments; A.R. contributed new reagents; M.K. analyzed data; M.K., F.T.C. and J.v.N. wrote the paper.

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Correspondence to John van Noort.

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Kruithof, M., Chien, FT., Routh, A. et al. Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber. Nat Struct Mol Biol 16, 534–540 (2009). https://doi.org/10.1038/nsmb.1590

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