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A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling

Nature Structural & Molecular Biology volume 12, pages 683–690 (2005)Cite this article

Abstract

The ATPase ISWI is the molecular motor of several nucleosome remodeling complexes including ACF. We analyzed the ACF-nucleosome interactions and determined the characteristics of ACF-dependent nucleosome remodeling. In contrast to ISWI, ACF interacts symmetrically with DNA entry sites of the nucleosome. Two-color fluorescence cross-correlation spectroscopy measurements show that ACF can bind four DNA duplexes simultaneously in a complex that contains two Acf1 and ISWI molecules. Using bead-bound nucleosomal substrates, nucleosome movement by mechanisms involving DNA twisting was excluded. Furthermore, an ACF-dependent local detachment of DNA from the nucleosome was demonstrated in a novel assay based on the preferred intercalation of ethidium bromide to free DNA. The findings suggest a loop recapture mechanism in which ACF introduces a DNA loop at the nucleosomal entry site that propagates over the histone octamer surface and leads to nucleosome repositioning.

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Figure 1: ACF interacts with the DNA entry site of the nucleosome.
Figure 2: Analysis of ACF-DNA binding by fluorescence cross-correlation spectroscopy.
Figure 3: High-resolution analysis of the nucleosome remodeling reaction.
Figure 4: Large obstacles do not inhibit nucleosome remodeling.
Figure 5: ACF-dependent nucleosome remodeling generates accessible DNA.
Figure 6: Scheme of the local recapture model.

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Acknowledgements

We thank H. Emmerichs from Spectra Physics for providing the laser equipment and Leica Microsystems for making the FCS system available. This work was supported by grants from Deutsche Forschungsgemeinschaft and the Volkswagen Foundation in the program Junior Research Groups at German Universities.

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Authors and Affiliations

  1. Adolf-Butenandt-Institut, Molekularbiologie, Schillerstrasse 44, München, 80336, Germany

    Ralf Strohner, Karoline Dachauer, Julia Hochstatter & Gernot Längst

  2. Kirchhoff-Institut für Physik, AG Molekulare Biophysik, Im Neuenheimer Feld 227, Heidelberg, 69120, Germany

    Malte Wachsmuth, Jacek Mazurkiewicz & Karsten Rippe

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Supplementary information

Supplementary Fig. 1

ACF has an apparent molecular mass above 600 kDa. (PDF 2462 kb)

Supplementary Fig. 2

Nucleosome remodeling does not release biotinylated nucleosomes from Streptavidin beads. (PDF 964 kb)

Supplementary Methods (PDF 909 kb)

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Strohner, R., Wachsmuth, M., Dachauer, K. et al. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat Struct Mol Biol 12, 683–690 (2005). https://doi.org/10.1038/nsmb966

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