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Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules

Nature Structural & Molecular Biology volume 13, pages 549–554 (2006)Cite this article

Abstract

Chromatin-remodeling enzymes can overcome strong histone-DNA interactions within the nucleosome to regulate access of DNA-binding factors to the genetic code. By unzipping individual DNA duplexes, each containing a uniquely positioned nucleosome flanked by long segments of DNA, we directly probed histone-DNA interactions. The resulting disruption-force signatures were characteristic of the types and locations of interactions and allowed measurement of the positions of nucleosomes with 2.6-base-pair (bp) precision. Nucleosomes remodeled by yeast SWI/SNF were moved bidirectionally along the DNA, resulting in a continuous position distribution. The characteristic distance of motion was ∼28 bp per remodeling event, and each event occurred with a catalytic efficiency of 0.4 min−1 per nM SWI/SNF. Remodeled nucleosomes had essentially identical disruption signatures to those of unremodeled nucleosomes, indicating that their overall structure remained canonical. These results impose substantial constraints on the mechanism of SWI/SNF remodeling.

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Figure 1: Experimental setup and raw data.
Figure 2: Unzipping through unremodeled and remodeled nucleosomes.
Figure 3: Kinetics of SWI/SNF-catalyzed nucleosome remodeling.

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Acknowledgements

We thank M. Hall for help with data analysis, L. Bai, J. Jin, B. Brower-Toland, R.M. Fulbright, D. Wacker, J. Tang, V. Elser and J.P. Sethna for helpful suggestions, members of the Wang laboratory for critical comments on the manuscript, J. Widom (Northwestern University) and R. Landick (University of Wisconsin) for gifts of plasmids and the National Cell Culture Center for HeLa cells. This research was supported by US National Institutes of Health grants to J.T.L, C.L.P. and M.D.W and the Keck Foundation's Distinguished Young Scholar Award to M.D.W.

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Authors and Affiliations

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

    Alla Shundrovsky & Michelle D Wang

  2. University of Massachusetts Medical School, Program in Molecular Medicine, Worcester, 01605, Massachusetts, USA

    Corey L Smith & Craig L Peterson

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

    John T Lis

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  1. Alla Shundrovsky
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Correspondence to Michelle D Wang.

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Supplementary information

Supplementary Fig. 1

Cross-correlation position alignment (PDF 80 kb)

Supplementary Fig. 2

Examples of individual traces of disruption force vs. number of base pairs unzipped (PDF 56 kb)

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Shundrovsky, A., Smith, C., Lis, J. et al. Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat Struct Mol Biol 13, 549–554 (2006). https://doi.org/10.1038/nsmb1102

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