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High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

Nature Structural & Molecular Biology volume 16, pages 124–129 (2009)Cite this article

Abstract

The nature of the nucleosomal barrier that regulates access to the underlying DNA during many cellular processes is not fully understood. Here we present a detailed map of histone-DNA interactions along the DNA sequence to near base pair accuracy by mechanically unzipping single molecules of DNA, each containing a single nucleosome. This interaction map revealed a distinct ∼5-bp periodicity that was enveloped by three broad regions of strong interactions, with the strongest occurring at the dyad and the other two about ±40-bp from the dyad. Unzipping up to the dyad allowed recovery of a canonical nucleosome upon relaxation of the DNA, but unzipping beyond the dyad resulted in removal of the histone octamer from its initial DNA sequence. These findings have important implications for how RNA polymerase and other DNA-based enzymes may gain access to DNA associated with a nucleosome.

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Figure 1: Nucleosome disruptions under a constant unzipping force.
Figure 2: Histone-DNA interaction map within a nucleosome core particle.
Figure 3: Nucleosome disruptions under a constant loading rate.
Figure 4: Mechanical unzipping (left) to mimic motor enzyme progression into a nucleosome (right).

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Acknowledgements

We thank members of the Wang laboratory and B. Brower-Toland for critical reading of the manuscript, J. Jin for helpful advice with biochemical preparations and D.S. Johnson for helpful discussions on instrumentation. We wish to acknowledge support from the US National Institutes of Health (GM059849 to M.D.W.; GM25232 to J.T.L.), the Keck Foundation (to M.D.W.), the Cornell Nanobiotechnology Center (to M.D.W. and J.T.L.) and the Molecular Biophysics Training Grant Traineeship (to M.A.H.).

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Author notes

  1. Alla Shundrovsky & Lu Bai

    Present address: Present addresses: Department of Mechanical Engineering, Yale University, New Haven, Connecticut 06511, USA (A.S.); Rockefeller University, 1230 York Avenue, New York, New York 10065, USA (L.B.).,

Authors and Affiliations

  1. Department of Physics—Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, 14853, New York, USA.

    Michael A Hall, Alla Shundrovsky, Lu Bai, Robert M Fulbright & Michelle D Wang

  2. Department of Molecular Biology and Genetics, Cornell University, Ithaca, 14853, New York, USA.

    John T Lis

  3. Howard Hughes Medical Institute, Cornell University, Ithaca, 14853, New York, USA.

    Michelle D Wang

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Correspondence to Michelle D Wang.

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Hall, M., Shundrovsky, A., Bai, L. et al. High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol 16, 124–129 (2009). https://doi.org/10.1038/nsmb.1526

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