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Dynamics of nucleosome remodelling by individual ACF complexes

Abstract

The ATP-dependent chromatin assembly and remodelling factor (ACF) functions to generate regularly spaced nucleosomes, which are required for heritable gene silencing. The mechanism by which ACF mobilizes nucleosomes remains poorly understood. Here we report a single-molecule FRET study that monitors the remodelling of individual nucleosomes by ACF in real time, revealing previously unknown remodelling intermediates and dynamics. In the presence of ACF and ATP, the nucleosomes exhibit gradual translocation along DNA interrupted by well-defined kinetic pauses that occurred after approximately seven or three to four base pairs of translocation. The binding of ACF, translocation of DNA and exiting of translocation pauses are all ATP-dependent, revealing three distinct functional roles of ATP during remodelling. At equilibrium, a continuously bound ACF complex can move the nucleosome back-and-forth many times before dissociation, indicating that ACF is a highly processive and bidirectional nucleosome translocase.

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Figure 1: Monitoring ACF-catalysed nucleosome remodelling by single-molecule FRET.
Figure 2: Real-time dynamics of ACF-catalysed nucleosome translocation.
Figure 3: ACF-catalysed nucleosome translocation is interrupted by well defined kinetic pauses.
Figure 4: ACF catalyses processive and bidirectional nucleosome translocation.

References

  1. Becker, P. B. & Horz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247–273 (2002)

    CAS  Article  Google Scholar 

  2. Narlikar, G. J., Fan, H. Y. & Kingston, R. E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475–487 (2002)

    CAS  Article  Google Scholar 

  3. Flaus, A. & Owen-Hughes, T. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14, 165–173 (2004)

    CAS  Article  Google Scholar 

  4. Smith, C. L. & Peterson, C. L. ATP-dependent chromatin remodeling. Curr. Top. Dev. Biol. 65, 115–148 (2004)

    Article  Google Scholar 

  5. Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273–304 (2009)

    CAS  Article  Google Scholar 

  6. Saha, A., Wittmeyer, J. & Cairns, B. R. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 16, 2120–2134 (2002)

    CAS  Article  Google Scholar 

  7. 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)

    CAS  Article  Google Scholar 

  8. Tsukiyama, T., Palmer, J., Landel, C. C., Shiloach, J. & Wu, C. Characterization of the Imitation Switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae . Genes Dev. 13, 686–697 (1999)

    CAS  Article  Google Scholar 

  9. Hamiche, A., Sandaltzopoulos, R., Gdula, D. A. & Wu, C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 97, 833–842 (1999)

    CAS  Article  Google Scholar 

  10. 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)

    Article  Google Scholar 

  11. Kassabov, S. R., Henry, N. M., Zofall, M., Tsukiyama, T. & Bartholomew, B. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22, 7524–7534 (2002)

    CAS  Article  Google Scholar 

  12. Zhang, Y. et al. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol. Cell 24, 559–568 (2006)

    CAS  Article  Google Scholar 

  13. Lia, G. et al. Direct observation of DNA distortion by the RSC complex. Mol. Cell 21, 417–425 (2006)

    CAS  Article  Google Scholar 

  14. Shundrovsky, A., Smith, C. L., Lis, J. T., Peterson, C. L. & Wang, M. D. Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nature Struct. Mol. Biol. 13, 549–554 (2006)

    CAS  Article  Google Scholar 

  15. Stryer, L. & Haugland, R. P. Energy transfer: a spectroscopic ruler. Proc. Natl Acad. Sci. USA 58, 719–726 (1967)

    ADS  CAS  Article  Google Scholar 

  16. Ha, T. et al. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl Acad. Sci. USA 93, 6264–6268 (1996)

    ADS  CAS  Article  Google Scholar 

  17. Zhuang, X. et al. A single molecule study of RNA catalysis and folding. Science 288, 2048–2051 (2000)

    ADS  CAS  Article  Google Scholar 

  18. 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)

    CAS  Article  Google Scholar 

  19. 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)

    CAS  Article  Google Scholar 

  20. 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)

    ADS  CAS  Article  Google Scholar 

  21. LeRoy, G., Loyola, A., Lane, W. S. & Reinberg, D. Purification and characterization of a human factor that assembles chromatin. J. Biol. Chem. 275, 14787–14790 (2000)

    CAS  Article  Google Scholar 

  22. 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)

    CAS  Article  Google Scholar 

  23. 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)

    CAS  Article  Google Scholar 

  24. 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)

    CAS  Article  Google Scholar 

  25. Abbondanzieri, E. A. et al. Dynamic binding orientations direct activity of HIV reverse transcriptase. Nature 453, 184–189 (2008)

    ADS  CAS  Article  Google Scholar 

  26. 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)

    CAS  Article  Google Scholar 

  27. 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)

    CAS  Article  Google Scholar 

  28. 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)

    CAS  Article  Google Scholar 

  29. 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)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  31. Li, G., Levitus, M., Bustamante, C. & Widom, J. Rapid spontaneous accessibility of nucleosomal DNA. Nature Struct. Mol. Biol. 12, 46–53 (2004)

    Article  Google Scholar 

  32. Partensky, P. D. & Narlikar, G. J. Chromatin remodelers act globally, sequence positions nucleosomes locally. J. Mol. Biol. 391, 12–25 (2009)

    CAS  Article  Google Scholar 

  33. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997)

    ADS  CAS  Article  Google Scholar 

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

    ADS  Article  Google Scholar 

  35. 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)

    CAS  Article  Google Scholar 

  36. Raki, L. R. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature 10.1038/nature08621 (this issue)

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

    CAS  Article  Google Scholar 

  38. Fitzgerald, D. J. et al. Reaction cycle of the yeast Isw2 chromatin remodeling complex. EMBO J. 23, 3836–3843 (2004)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  40. Luger, K., Rechsteiner, T. J. & Richmond, T. J. Preparation of nucleosome core particle from recombinant histones. Methods Enzymol. 304, 3–19 (1999)

    CAS  Article  Google Scholar 

  41. 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)

    CAS  Article  Google Scholar 

  42. Rasnik, I., McKinney, S. A. & Ha, T. Nonblinking and long-lasting single-molecule fluorescence imaging. Nature Methods 3, 891–893 (2006)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank J. Widom for providing the plasmid containing the 601 positioning sequence and R. E. Kingston for the plasmids containing the SNF2h and Acf1 genes. We also thank L. Racki and E. Abbondanzieri for helpful discussions, and W. Huang and B. Harada for help with some experiments. This work is supported in part by Howard Hughes Medical Institute (to X.Z.) and the National Institutes of Health (GM073767) and the Beckman Foundation (to G.J.N). X.Z. is a Howard Hughes Medical Institute investigator. M.D.S. was a NIH Ruth L. Kirschstein NSRA Fellow, G.J.N is a Leukemia and Lymphoma Society Scholar.

Author Contributions T.R.B. performed the experiments and analysis with help from M.D.S.; J.G.Y. made the enzymes and histone proteins. T.R.B., G.J.N. and X.Z. designed the experiments. X.Z. oversaw the project.

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Correspondence to Geeta J. Narlikar or Xiaowei Zhuang.

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Blosser, T., Yang, J., Stone, M. et al. Dynamics of nucleosome remodelling by individual ACF complexes. Nature 462, 1022–1027 (2009). https://doi.org/10.1038/nature08627

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