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Dynamics of ATP-dependent chromatin assembly by ACF

Abstract

The assembly of DNA into chromatin is a critical step in the replication and repair of the eukaryotic genome1,2,3,4,5,6,7,8. It has been known for nearly 20 years that chromatin assembly is an ATP-dependent process9. ATP-dependent chromatin-assembly factor (ACF) uses the energy of ATP hydrolysis for the deposition of histones into periodic nucleosome arrays, and the ISWI subunit of ACF is an ATPase that is related to helicases10,11. Here we show that ACF becomes committed to the DNA template upon initiation of chromatin assembly. We also observed that ACF assembles nucleosomes in localized arrays, rather than randomly distributing them. By using a purified ACF-dependent system for chromatin assembly, we found that ACF hydrolyses about 2–4 molecules of ATP per base pair in the assembly of nucleosomes. This level of ATP hydrolysis is similar to that used by DNA helicases for the unwinding of DNA12. These results suggest that a tracking mechanism exists in which ACF assembles chromatin as an ATP-driven DNA-translocating motor. Moreover, this proposed mechanism for ACF may be relevant to the function of other chromatin-remodelling factors that contain ISWI subunits.

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Figure 1: Template commitment by ACF during chromatin assembly.
Figure 2: ACF remains committed to the DNA template for about 15–30 min.
Figure 3: Template commitment by ACF requires continual nucleosome assembly.
Figure 4: Partial chromatin assembly by ACF reveals template commitment and localized arrays of nucleosomes.
Figure 5: Chromatin assembly by ACF consumes about 270–640 molecules of ATP per nucleosome.

References

  1. Tsukiyama, T. & Wu, C. Chromatin remodeling and transcription. Curr. Opin. Genet. Dev. 7, 182–191 (1997)

    CAS  Article  Google Scholar 

  2. Cairns, B. R. Chromatin remodeling machines: similar motors, ulterior motives. Trends Biochem. Sci. 23, 20–25 (1998)

    CAS  Article  Google Scholar 

  3. Kornberg, R. D. & Lorch, Y. Chromatin-modifying and -remodeling complexes. Curr. Opin. Genet. Dev. 9, 148–151 (1999)

    CAS  Article  Google Scholar 

  4. Kingston, R. E. & Narlikar, G. J. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13, 2339–2352 (1999)

    CAS  Article  Google Scholar 

  5. Fyodorov, D. V. & Kadonaga, J. T. The many faces of chromatin remodeling: SWItching beyond transcription. Cell 106, 523–525 (2001)

    CAS  Article  Google Scholar 

  6. Vignali, M., Hassan, A. H., Neely, K. E. & Workman, J. L. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol. 20, 1899–1910 (2000)

    CAS  Article  Google Scholar 

  7. Fry, C. J. & Peterson, C. L. Chromatin remodeling enzymes: who's on first? Curr. Biol. 11, R185–R197 (2001)

    CAS  Article  Google Scholar 

  8. Flaus, A. & Owen-Hughes, T. Mechanisms for ATP-dependent chromatin remodeling. Curr. Opin. Genet. Dev. 11, 148–154 (2001)

    CAS  Article  Google Scholar 

  9. Glikin, G. C., Ruberti, I. & Worcel, A. Chromatin assembly in Xenopus oocytes: in vitro studies. Cell 37, 33–41 (1984)

    CAS  Article  Google Scholar 

  10. 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 

  11. 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 

  12. Lohman, T. M. & Bjornson, K. P. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65, 169–214 (1996)

    CAS  Article  Google Scholar 

  13. Gorbalenya, A. W. & Koonin, E. V. Helicases: amino acid sequence comparisons and structure–function relationships. Curr. Opin. Struct. Biol. 3, 419–429 (1993)

    CAS  Article  Google Scholar 

  14. Eisen, J. A., Sweder, K. S. & Hanawalt, P. C. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23, 2715–2723 (1995)

    CAS  Article  Google Scholar 

  15. Eggleston, A. K., O'Neill, T. E., Bradbury, E. M. & Kowalczykowski, S. C. Unwinding of nucleosomal DNA by a DNA helicase. J. Biol. Chem. 270, 2024–2031 (1995)

    CAS  Article  Google Scholar 

  16. Ramsperger, U. & Stahl, H. Unwinding of chromatin by the SV40 large T antigen DNA helicase. EMBO J. 14, 3215–3225 (1995)

    CAS  Article  Google Scholar 

  17. Adams, C. R. & Kamakaka, R. T. Chromatin assembly: biochemical identities and genetic redundancy. Curr. Opin. Genet. Dev. 9, 185–190 (1999)

    CAS  Article  Google Scholar 

  18. Verreault, A. De novo nucleosome assembly: new pieces in an old puzzle. Genes Dev. 14, 1430–1438 (2000)

    CAS  PubMed  Google Scholar 

  19. Mello, J. A. & Almouzhi, G. The ins and outs of nucleosome assembly. Curr. Opin. Genet. Dev. 11, 136–141 (2001)

    CAS  Article  Google Scholar 

  20. Velankar, S. S., Soultanas, P., Dillingham, M. S., Subramanya, H. S. & Wigley, D. B. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75–84 (1999)

    CAS  Article  Google Scholar 

  21. Havas, K. et al. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell 103, 1133–1142 (2000)

    CAS  Article  Google Scholar 

  22. Studitsky, V. M., Clark, D. J. & Felsenfeld, G. Overcoming a nucleosomal barrier to transcription. Cell 83, 19–27 (1995)

    CAS  Article  Google Scholar 

  23. Kornberg, R. D. & Lorch, Y. Interplay between chromatin structure and transcription. Curr. Opin. Cell Biol. 7, 371–375 (1995)

    CAS  Article  Google Scholar 

  24. Pazin, M. J. & Kadonaga, J. T. SWI2/SNF2 and related proteins: ATP-driven motors that disrupt protein–DNA interactions? Cell 88, 737–740 (1997)

    CAS  Article  Google Scholar 

  25. 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 

  26. Längst, G., Bonte, E. J., Corona, D. F. V. & 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 

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

    CAS  Article  Google Scholar 

  28. Whitehouse, I. et al. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature 400, 784–787 (1999)

    ADS  CAS  Article  Google Scholar 

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Acknowledgements

We thank P. Geiduschek, R. Dutnall, L. Pillus, T. Juven-Gershon, V. Alexiadis, T. Boulay, B. Santoso, A. Lusser, J. Huang Parsons and M. Levenstein for critical reading of the manuscript. This work was supported by a grant from the National Institutes of Health to J.T.K. D.V.F. is an American Cancer Society Postdoctoral Fellow.

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Correspondence to James T. Kadonaga.

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Fyodorov, D., Kadonaga, J. Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418, 896–900 (2002). https://doi.org/10.1038/nature00929

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