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Chromatin remodeling through directional DNA translocation from an internal nucleosomal site

Nature Structural & Molecular Biology volume 12, pages 747–755 (2005)Cite this article

Abstract

The RSC chromatin remodeler contains Sth1, an ATP-dependent DNA translocase. On DNA substrates, RSC/Sth1 tracks along one strand of the duplex with a 3′ → 5′ polarity and a tracking requirement of one base, properties that may enable directional DNA translocation on nucleosomes. The binding of RSC or Sth1 elicits a DNase I–hypersensitive site approximately two DNA turns from the nucleosomal dyad, and the binding of Sth1 requires intact DNA at this location. Results with various nucleosome substrates suggest that RSC/Sth1 remains at a fixed position on the histone octamer and that Sth1 conducts directional DNA translocation from a location about two turns from the nucleosomal dyad, drawing in DNA from one side of the nucleosome and pumping it toward the other. These studies suggest that nucleosome mobilization involves directional DNA translocation initiating from a fixed internal site on the nucleosome.

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Figure 1: RSC binds the nucleosome core and the Sth1 ATPase domain elicits a DNase I–hypersensitive site about two turns from the nucleosomal dyad.
Figure 2: Treatment of remodeled nucleosomes with restriction endonuclease leads to the release of the smaller cleaved fragment.
Figure 3: A DNA linker on one side of the nucleosome enables restriction enzyme access to sites on the opposite side of the dyad.
Figure 4: Small gaps present in one DNA strand on the nucleosome affect restriction enzyme accessibility in a position-dependent manner.
Figure 5: DNA gaps positioned two turns from the dyad affect binding by Sth1 and remodeling by RSC.
Figure 6: RSC is a 3′ → 5′ DNA translocase with a tracking requirement of one base.
Figure 7: Models for DNA translocation on nucleosomes.

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Acknowledgements

We thank B. Schackmann for oligonucleotide syntheses, B. Kingston and G. Narlikar for the TGT plasmids, D. Close and C. Hill for purification of the Sth1301–1097 derivative and both M. Gordon and T. Formosa for comments on the manuscript. This work was funded by the US National Institutes of Health grant GM60415 (to B.R.C. and a majority of the support for A.S.), a University of Utah Graduate Research Fellowship (to A.S.), the Huntsman Cancer Institute (to J.W. and grant CA24014 for the support of core facilities) and the Howard Hughes Medical Institute (to B.R.C.).

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  1. Howard Hughes Medical Institute and the Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, 84112, Utah, USA

    Anjanabha Saha, Jacqueline Wittmeyer & Bradley R Cairns

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  1. Anjanabha Saha
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Correspondence to Bradley R Cairns.

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Supplementary information

Supplementary Fig. 1

RSC binding to nucleosomes bearing linker of different lengths. (PDF 88 kb)

Supplementary Methods (PDF 46 kb)

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Saha, A., Wittmeyer, J. & Cairns, B. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat Struct Mol Biol 12, 747–755 (2005). https://doi.org/10.1038/nsmb973

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