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Nucleosomes facilitate their own invasion

Nature Structural & Molecular Biology volume 11, pages 763–769 (2004)Cite this article

Abstract

DNA wrapped in nucleosomes is sterically occluded, creating obstacles for polymerase, regulatory, remodeling, repair and recombination complexes, which require access to the wrapped DNA. How such complexes recognize and gain access to their DNA target sites is not known. Here we report the direct detection of a dynamic equilibrium conformational transition in nucleosomes that greatly increases the distance between the end of the nucleosomal DNA and the histone core. We quantified the equilibrium constant for this transition under physiological conditions. As predicted by these findings, addition of LexA protein to nucleosomes containing the LexA target site drives this conformational equilibrium toward the unwrapped, accessible state, simultaneously allowing stable LexA binding. This inherent property of nucleosomes allows any protein, whether an energy-dependent machine or a passive binder, to gain access even to buried stretches of nucleosomal DNA.

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Figure 1: FRET systems for analysis of equilibrium conformational changes of nucleosomal DNA.
Figure 2: Dynamic equilibrium unwrapping of nucleosomal DNA in physiological [NaCl].
Figure 3: Site-specific protein binding is linked to partial DNA unwrapping.
Figure 4: Native gel analysis for LexA binding to naked DNA and nucleosomes.
Figure 5: Model linking equilibrium conformational fluctuations of nucleosomes to nucleosome activity.

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Acknowledgements

We thank T. Richmond and J. Hayes for X. laevis histone expression plasmids and J. Little for the LexA expression plasmid. We acknowledge the use of instruments in the Keck Biophysics Facility at Northwestern University. This work was supported by grants from the US National Institutes of Health to J.W.

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  1. Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, 60208-3500, Illinois, USA

    Gu Li & Jonathan Widom

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  1. Gu Li
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Correspondence to Jonathan Widom.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

[Mg2+] negligibly affects DNA unwrapping in physiological [NaCl]. (PDF 52 kb)

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Li, G., Widom, J. Nucleosomes facilitate their own invasion. Nat Struct Mol Biol 11, 763–769 (2004). https://doi.org/10.1038/nsmb801

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