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The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing

Nature Structural & Molecular Biology volume 13, pages 1078–1083 (2006)Cite this article

Abstract

Arrays of regularly spaced nucleosomes directly correlate with closed chromatin structures at silenced loci. The ATP-dependent chromatin-assembly factor (ACF) generates such arrays in vitro and is required for transcriptional silencing in vivo. A key unresolved question is how ACF 'measures' equal spacing between nucleosomes. We show that ACF senses flanking DNA length and transduces length information in an ATP-dependent manner to regulate the rate of nucleosome movement. Using fluorescence resonance energy transfer to follow nucleosome movement, we find that ACF can rapidly sample DNA on either side of a nucleosome and moves the longer flanking DNA across the nucleosome faster than the shorter flanking DNA. This generates a dynamic equilibrium in which nucleosomes having equal DNA on either side accumulate. Our results indicate that ACF generates the characteristic 50- to 60-base-pair internucleosomal spacing in silent chromatin by kinetically discriminating against shorter linker DNAs.

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Figure 1: ACF efficiently centers mononucleosomes.
Figure 2: Use of FRET to visualize nucleosome movement in real time.
Figure 3: ACF kinetically discriminates between different flanking DNA lengths.
Figure 4: Model for nucleosome centering by ACF.
Figure 5: Testing the predictions of the model.

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Acknowledgements

We thank J. Widom (Northwestern University) for the 601 plasmid, J.J. Hayes (University of Rochester Medical Center) for the 5S plasmid, H.-Y. Fan and R.E. Kingston (Harvard Medical School) for SNF2h and ACF1 constructs, R.D. Mullins (University of California, San Francisco) for use of the fluorometer, K. Ashrafi, H.-Y. Fan, J.T. Kadonaga, B. Panning, A.K. Srivastava, J.S. Weissman, J. Widom, C. Wu and K.R. Yamamoto for helpful comments on the manuscript and members of the Narlikar lab for technical advice and discussion. J.G.Y. is supported by a US National Science Foundation Graduate Research Fellowship. This work was supported in part by a grant from the US National Institutes of Health (to G.J.N.).

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  1. Janet G Yang and Tina Shahian Madrid: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, 94158, California, USA

    Janet G Yang, Tina Shahian Madrid, Elena Sevastopoulos & Geeta J Narlikar

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Contributions

J.G.Y., T.S.M. and G.J.N. designed the experiments, J.G.Y. and T.S.M. did the experiments and analyzed the data, E.S. made reagents for the experiments and J.G.Y. and G.J.N. interpreted the data and wrote the manuscript.

Corresponding author

Correspondence to Geeta J Narlikar.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Mapping histone octamer positions of mononucleosome substrates. (PDF 688 kb)

Supplementary Fig. 2

An alternative model for hACF centering. (PDF 175 kb)

Supplementary Fig. 3

Modeling mononucleosome centering by hACF. (PDF 389 kb)

Supplementary Fig. 4

Kinetics of remodeling at 2 mM ATP. (PDF 88 kb)

Supplementary Fig. 5

hACF remodeling is sequence independent. (PDF 167 kb)

Supplementary Fig. 6

hACF activity on 601 nucleosomes with varying flanking DNA lengths. (PDF 287 kb)

Supplementary Fig. 7

Restriction enzyme accessibility experiment. (PDF 68 kb)

Supplementary Fig. 8

Model for centering assuming hACF is a dimer. (PDF 71 kb)

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Yang, J., Madrid, T., Sevastopoulos, E. et al. The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nat Struct Mol Biol 13, 1078–1083 (2006). https://doi.org/10.1038/nsmb1170

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