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

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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.

References

  1. 1

    Corona, D. F. et al. ISWI regulates higher-order chromatin structure and histone H1 assembly in vivo . PLoS Biol. 5, e232 (2007)

  2. 2

    Fyodorov, D. V., Blower, M. D., Karpen, G. H. & Kadonaga, J. T. Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo . Genes Dev. 18, 170–183 (2004)

  3. 3

    Ito, T., Bulger, M., Pazin, M. J., Kobayashi, R. & Kadonaga, J. T. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90, 145–155 (1997)

  4. 4

    Varga-Weisz, P. D. et al. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388, 598–602 (1997)

  5. 5

    Deuring, R. et al. The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo . Mol. Cell 5, 355–365 (2000)

  6. 6

    Poot, R. A. et al. HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. EMBO J. 19, 3377–3387 (2000)

  7. 7

    Bochar, D. A. et al. A family of chromatin remodeling factors related to Williams syndrome transcription factor. Proc. Natl Acad. Sci. USA 97, 1038–1043 (2000)

  8. 8

    Yang, J. G., Madrid, T. S., Sevastopoulos, E. & Narlikar, G. J. The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nature Struct. Mol. Biol. 13, 1078–1083 (2006)

  9. 9

    Kagalwala, M. N., Glaus, B. J., Dang, W., Zofall, M. & Bartholomew, B. Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 23, 2092–2104 (2004)

  10. 10

    Sun, F. L., Cuaycong, M. H. & Elgin, S. C. Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin. Mol. Cell. Biol. 21, 2867–2879 (2001)

  11. 11

    Corona, D. F. et al. ISWI is an ATP-dependent nucleosome remodeling factor. Mol. Cell 3, 239–245 (1999)

  12. 12

    Aalfs, J. D., Narlikar, G. J. & Kingston, R. E. Functional differences between the human ATP-dependent nucleosome remodeling proteins BRG1 and SNF2H. J. Biol. Chem. 276, 34270–34278 (2001)

  13. 13

    Eberharter, A. et al. Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. EMBO J. 20, 3781–3788 (2001)

  14. 14

    Längst, G., Bonte, E. J., Corona, D. F. & Becker, P. B. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97, 843–852 (1999)

  15. 15

    Ito, T. et al. ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev. 13, 1529–1539 (1999)

  16. 16

    Dürr, H., Flaus, A., Owen-Hughes, T. & Hopfner, K. P. Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures. Nucleic Acids Res. 34, 4160–4167 (2006)

  17. 17

    Dang, W. & Bartholomew, B. Domain architecture of the catalytic subunit in the ISW2-nucleosome complex. Mol. Cell. Biol. 27, 8306–8317 (2007)

  18. 18

    Grüne, T. et al. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell 12, 449–460 (2003)

  19. 19

    Clapier, C. R., Langst, G., Corona, D. F., Becker, P. B. & Nightingale, K. P. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol. Cell. Biol. 21, 875–883 (2001)

  20. 20

    Clapier, C. R., Nightingale, K. P. & Becker, P. B. A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 30, 649–655 (2002)

  21. 21

    Hamiche, A., Kang, J. G., Dennis, C., Xiao, H. & Wu, C. Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF. Proc. Natl Acad. Sci. USA 98, 14316–14321 (2001)

  22. 22

    Fazzio, T. G., Gelbart, M. E. & Tsukiyama, T. Two distinct mechanisms of chromatin interaction by the Isw2 chromatin remodeling complex in vivo . Mol. Cell. Biol. 25, 9165–9174 (2005)

  23. 23

    Ferreira, H., Flaus, A. & Owen-Hughes, T. Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms. J. Mol. Biol. 374, 563–579 (2007)

  24. 24

    Dang, W., Kagalwala, M. N. & Bartholomew, B. Regulation of ISW2 by concerted action of the histone H4 tail and extranucleosomal DNA. Mol. Cell. Biol. 26, 7388–7396 (2006)

  25. 25

    Shogren-Knaak, M. et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847 (2006)

  26. 26

    Rice, S. et al. A structural change in the kinesin motor protein that drives motility. Nature 402, 778–784 (1999)

  27. 27

    Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19–42 (1998)

  28. 28

    Naber, N., Purcell, T. J., Pate, E. & Cooke, R. Dynamics of the nucleotide pocket of myosin measured by spin-labeled nucleotides. Biophys. J. 92, 172–184 (2007)

  29. 29

    Rice, S. et al. Thermodynamic properties of the kinesin neck-region docking to the catalytic core. Biophys. J. 84, 1844–1854 (2003)

  30. 30

    Schwanbeck, R., Xiao, H. & Wu, C. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J. Biol. Chem. 279, 39933–39941 (2004)

  31. 31

    Lohman, T. M., Thorn, K. & Vale, R. D. Staying on track: common features of DNA helicases and microtubule motors. Cell 93, 9–12 (1998)

  32. 32

    Chin, J., Langst, G., Becker, P. B. & Widom, J. Fluorescence anisotropy assays for analysis of ISWI-DNA and ISWI-nucleosome interactions. Methods Enzymol. 376, 3–16 (2003)

  33. 33

    Dürr, H., Korner, C., Muller, M., Hickmann, V. & Hopfner, K. P. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121, 363–373 (2005)

  34. 34

    Thomä, N. H. et al. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nature Struct. Mol. Biol. 12, 350–356 (2005)

  35. 35

    Radermacher, M. et al. Cryo-electron microscopy and three-dimensional reconstruction of the calcium release channel/ryanodine receptor from skeletal muscle. J. Cell Biol. 127, 411–423 (1994)

  36. 36

    Stockdale, C., Flaus, A., Ferreira, H. & Owen-Hughes, T. Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J. Biol. Chem. 281, 16279–16288 (2006)

  37. 37

    Zofall, M., Persinger, J., Kassabov, S. R. & Bartholomew, B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nature Struct. Mol. Biol. 13, 339–346 (2006)

  38. 38

    Whitehouse, I., Stockdale, C., Flaus, A., Szczelkun, M. D. & Owen-Hughes, T. Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme. Mol. Cell. Biol. 23, 1935–1945 (2003)

  39. 39

    Cairns, B. R. Chromatin remodeling: insights and intrigue from single-molecule studies. Nature Struct. Mol. Biol. 14, 989–996 (2007)

  40. 40

    Strohner, R. et al. A ‘loop recapture’ mechanism for ACF-dependent nucleosome remodeling. Nature Struct. Mol. Biol. 12, 683–690 (2005)

  41. 41

    Längst, G. & Becker, P. B. Nucleosome remodeling: one mechanism, many phenomena? Biochim. Biophys. Acta 1677, 58–63 (2004)

  42. 42

    Racki, L. R. & Narlikar, G. J. ATP-dependent chromatin remodeling enzymes: two heads are not better, just different. Curr. Opin. Genet. Dev. 18, 137–144 (2008)

  43. 43

    Enemark, E. J. & Joshua-Tor, L. On helicases and other motor proteins. Curr. Opin. Struct. Biol. 18, 243–257 (2008)

  44. 44

    Blosser, T. R., Yang, J. G., Stone, M. D., Narlikar, G. J. & Zhuang, X. Dynamics of nucleosome remodelling by individual ACF complexes. Nature 10.1038/nature08627 (in the press)

  45. 45

    Fyodorov, D. V. & Kadonaga, J. T. Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418, 896–900 (2002)

  46. 46

    Gangaraju, V. K., Prasad, P., Srour, A., Kagalwala, M. N. & Bartholomew, B. Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2. Mol. Cell 35, 58–69 (2009)

  47. 47

    He, X., Fan, H. Y., Narlikar, G. J. & Kingston, R. E. Human ACF1 alters the remodeling strategy of SNF2h. J. Biol. Chem. 281, 28636–28647 (2006)

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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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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) doi:10.1038/nature08621

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