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Structure and mechanism of the chromatin remodelling factor ISW1a

Nature volume 472, pages 448–453 (2011)Cite this article

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Abstract

Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors are implicated in establishing the nucleosome repeat during replication and altering nucleosome position to affect gene activity. Here we have solved the crystal structures of S. cerevisiae ISW1a lacking its ATPase domain both alone and with DNA bound at resolutions of 3.25 Å and 3.60 Å, respectively, and we have visualized two different nucleosome-containing remodelling complexes using cryo-electron microscopy. The composite X-ray and electron microscopy structures combined with site-directed photocrosslinking analyses of these complexes suggest that ISW1a uses a dinucleosome substrate for chromatin remodelling. Results from a remodelling assay corroborate the dinucleosome model. We show how a chromatin remodelling factor could set the spacing between two adjacent nucleosomes acting as a ‘protein ruler’.

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Figure 1: ISW1a(ΔATPase) X-ray structure.
Figure 2: ISW1a(ΔATPase)–DNA X-ray structure.
Figure 3: ISW1a(ΔATPase)–mononucleosome cryo-EM structures.
Figure 4: Gel mobility and site-directed photocrosslinking of ISW1a(ΔATPase) bound to mononucleosomes.
Figure 5: Model of ISW1a(ΔATPase) bound to a dinucleosome and ISW1a remodelling reaction.

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Protein Data Bank

Data deposits

X-ray structures have been deposited in the Protein Data Bank under accession numbers 2y9y (ISW1a(ΔATPase)) and 2y9z (ISW1a(ΔATPase)–DNA), respectively. Cryo-EM maps have been deposited in the Electron Microscopy Data Bank under accession codes 1877 and 1878.

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Acknowledgements

We thank B. Blattmann for help in crystal screening (NCCR Structural Biology crystallization facility), C. Schulze-Briese and T. Tomizaki (SLS, Paul Scherrer Institute) for assistance in X-ray data collection, and the ETH Zurich Electron Microscopy Center for assistance in EM data collection. K.Y. appreciates support from the Toyobo Biofoundation and the Uehara Memorial Foundation, and discussion with T. Maier. T.J.R. is grateful to T. Tsukiyama for discussion and materials. We appreciate the financial support from the Swiss National Science Fond and the NCCR Structural Biology.

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Author notes

  1. Daniel J. Fitzgerald & Carl DeLuca

    Present address: Present addresses: Blueshift Pharma, Technoparkstrasse 1, CH-8005 Zürich, Switzerland (D.J.F.); Helix BioPharma Corp., 1036 Parsons Road, Edmonton, Alberta T6X 0J4, Canada (C.D.).,

  2. Kazuhiro Yamada, Timothy D. Frouws and Brigitte Angst: These authors contributed equally to this work.

Authors and Affiliations

  1. ETH Zürich, Institute of Molecular Biology and Biophysics, Schafmattstr. 20, CH-8093 Zürich, Switzerland

    Kazuhiro Yamada, Timothy D. Frouws, Brigitte Angst, Daniel J. Fitzgerald, Carl DeLuca, Kyoko Schimmele, David F. Sargent & Timothy J. Richmond

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Contributions

K.Y. was responsible for X-ray crystallography. T.D.F. was responsible for electron microscopy. B.A. was responsible for mobility assays, site-directed photocrosslinking and hydroxyl radical footprinting. D.J.F. and C.D. designed and expressed the first constructs of ISW1a(ΔATPase) and carried out biochemical analyses. K.Y. and B.A. designed the specific ISW1a constructs essential to the X-ray crystallography and electron microscopy, and to the photocrosslinking and footprinting, respectively. K.S. provided biochemical technical assistance. D.F.S. provided assistance for X-ray data collection. T.J.R. conceived the project, supervised and constructed the dinucleosome model. T.J.R. prepared the manuscript with major contributions from K.Y., T.D.F. and B.A. All authors discussed the results and commented on the manuscript.

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Correspondence to Timothy J. Richmond.

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Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-9 with legends and Supplementary Table 1.Supplementary Figures 7-9 were omitted when this paper first appeared online and were added on 06 May 2011. (PDF 16356 kb)

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Yamada, K., Frouws, T., Angst, B. et al. Structure and mechanism of the chromatin remodelling factor ISW1a. Nature 472, 448–453 (2011). https://doi.org/10.1038/nature09947

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