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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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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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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DOI: https://doi.org/10.1038/nsmb.1526
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