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The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes

Nature volume 462, pages 1016–1021 (2009)Cite this article

Abstract

Evenly spaced nucleosomes directly correlate with condensed chromatin and gene silencing. The ATP-dependent chromatin assembly factor (ACF) forms such structures in vitro and is required for silencing in vivo. ACF generates and maintains nucleosome spacing by constantly moving a nucleosome towards the longer flanking DNA faster than the shorter flanking DNA. How the enzyme rapidly moves back and forth between both sides of a nucleosome to accomplish bidirectional movement is unknown. Here we show that nucleosome movement depends cooperatively on two ACF molecules, indicating that ACF functions as a dimer of ATPases. Further, the nucleotide state determines whether the dimer closely engages one or both sides of the nucleosome. Three-dimensional reconstruction by single-particle electron microscopy of the ATPase–nucleosome complex in an activated ATP state reveals a dimer architecture in which the two ATPases face each other. Our results indicate a model in which the two ATPases work in a coordinated manner, taking turns to engage either side of a nucleosome, thereby allowing processive bidirectional movement. This novel dimeric motor mechanism differs from that of dimeric motors such as kinesin and dimeric helicases that processively translocate unidirectionally and reflects the unique challenges faced by motors that move nucleosomes.

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Figure 1: ATP state regulates immobilization of the histone H4 tail and proximal interactions.
Figure 2: SNF2h and ACF function as dimers of ATPases.
Figure 3: Visualization of SNF2h bound to the nucleosome in the presence of ADP•BeF x using electron microscopy.
Figure 4: Simple model for how a dimeric ACF moves nucleosomes.

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Acknowledgements

We thank J. Widom for the 601 plasmid. We thank H. Madhani, M. D. Simon, and members of the Narlikar laboratory for helpful discussion and comments on the manuscript. We thank R. Howard for help with equilibrium analytical ultracentrifugation; W. Ross, J. Lin, S. Hota and B. Bartholomew for advice on footprinting, and C. Cunningham for assistance with nucleosome depiction. This work was supported by grants from the Sandler Family Supporting Foundation (Sandler Opportunity Award and New Technology Award in Basic Science to Y.C., Program for Breakthrough Biomedical Research (PBBR) Award to G.J.N.), UCSF Academic Senate Shared Equipment Grant (to Y.C.), grants from the National Institutes of Health (to R.C. and G.J.N.) and by the Beckman Foundation (to G.J.N.). P.D.P. and J.G.Y. were supported by US National Science Foundation Graduate Research Fellowships. G.J.N. is a Leukemia and Lymphoma Society Scholar. G.J.N. wishes to acknowledge D. Herschlag’s generative mentorship.

Author Contributions. L.R.R. and J.G.Y. performed the bulk of the experiments. J.G.Y. performed the equilibrium analytical ultracentrifugation and footprinting experiments. L.R.R. performed the fluorescence-based binding and FRET-based activity assays. N.N. and L.R.R. performed the EPR-based experiments, P.D.P. helped design the EPR experiments, T.J.P. conducted the deconvolution analysis of the EPR data, and R.C. helped design and analyse the EPR experiments. Y.C. and L.R.R. designed and performed the electron microscopy-based experiments, and Y.C. and A.A. conducted the analysis of the electron microscopy data. L.R.R., J.G.Y. and G.J.N. designed and interpreted most of the experiments. L.R.R., J.G.Y., R.C., Y.C. and G.J.N. wrote the manuscript.

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  1. Lisa R. Racki and Janet G. Yang: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Biochemistry and Biophysics, University of California, 600 16th Street,

    Lisa R. Racki, Janet G. Yang, Nariman Naber, Peretz D. Partensky, Ashley Acevedo, Thomas J. Purcell, Roger Cooke, Yifan Cheng & Geeta J. Narlikar

  2. Department of Biochemistry and Biophysics, The W.M. Keck Advanced Microscopy Laboratory, University of California San Francisco, San Francisco, California 94158, USA,

    Yifan Cheng

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Correspondence to Yifan Cheng or Geeta J. Narlikar.

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Racki, L., Yang, J., Naber, N. et al. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature 462, 1016–1021 (2009). https://doi.org/10.1038/nature08621

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