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The Williams syndrome transcription factor interacts with PCNA to target chromatin remodelling by ISWI to replication foci

Nature Cell Biology volume 6, pages 1236–1244 (2004)Cite this article

Abstract

Chromatin states have to be faithfully duplicated during DNA replication to maintain cell identity. It is unclear whether or how ATP-dependent chromatin-remodelling factors are involved in this process. Here we provide evidence that the Williams syndrome transcription factor (WSTF) is targeted to replication foci through direct interaction with the DNA clamp PCNA, an important coordinator of DNA and chromatin replication. WSTF, in turn, recruits imitation switch (ISWI)-type nucleosome-remodelling factor SNF2H to replication sites. These findings reveal a novel recruitment mechanism for ATP-dependent chromatin-remodelling factors that is fundamentally different from the previously documented targeting by sequence-specific transcriptional regulators. RNA-interference-mediated depletion of WSTF or SNF2H causes a compaction of newly replicated chromatin and increases the amount of heterochromatin markers, including HP1β. This increase in the amount of HP1β protein is mediated by progression through S phase and is not the result of an increase in HP1β mRNA levels. We propose that the WSTF–ISWI complex has a role in the maintenance of chromatin structures during DNA replication.

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Figure 1: WSTF targets replication foci throughout S phase.
Figure 2: WSTF binds directly to PCNA and targets SNF2H.
Figure 3: WSTF binds to replication sites by interacting with PCNA.
Figure 4: SNF2H binds to replication sites by interacting with PCNA through WSTF.
Figure 5: Depletion of WSTF leads to chromatin compaction and increases the amount of chromatin-bound heterochromatin markers.

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References

  1. Ridgway, P. & Almouzni, G. CAF-1 and the inheritance of chromatin states: at the crossroads of DNA replication and repair. J. Cell Sci. 113, 2647–2658 (2000).

    CAS  PubMed  Google Scholar 

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

    CAS  Article  Google Scholar 

  3. Bozhenok, L., Wade, P. A. & Varga-Weisz, P. WSTF–ISWI chromatin remodeling complex targets heterochromatic replication foci. EMBO J. 21, 2231–2241 (2002).

    CAS  Article  Google Scholar 

  4. Dirscherl, S. S. & Krebs, J. E. Functional diversity of ISWI complexes. Biochem. Cell Biol. 82, 482–489 (2004).

    CAS  Article  Google Scholar 

  5. Francke, U. Williams-Beuren syndrome: genes and mechanisms. Hum. Mol. Genet. 8, 1947–1954 (1999).

    CAS  Article  Google Scholar 

  6. Kitagawa, H. et al. The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams Syndrome. Cell 113, 905–917 (2003).

    CAS  Article  Google Scholar 

  7. Collins, N. et al. An ACF1–ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. Nature Genet. 32, 627–632 (2002).

    CAS  Article  Google Scholar 

  8. McNairn, A. J. & Gilbert, D. M. Epigenomic replication: Linking epigenetics to DNA replication. Bioessays 25, 647–656 (2003).

    CAS  Article  Google Scholar 

  9. Maga, G. & Hubscher, U. Proliferating cell nuclear antigen (PCNA): a dancer with many partners. J. Cell Sci. 116, 3051–3060 (2003).

    CAS  Article  Google Scholar 

  10. Zheleva, D. I. et al. A quantitative study of the in vitro binding of the C-terminal domain of p21 to PCNA: affinity, stoichiometry, and thermodynamics. Biochemistry 39, 7388–7397 (2000).

    CAS  Article  Google Scholar 

  11. Gulbis, J. M., Kelman, Z., Hurwitz, J., O'Donnell, M. & Kuriyan, J. Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell 87, 297–306 (1996).

    CAS  Article  Google Scholar 

  12. Sporbert, A., Gahl, A., Ankerhold, R., Leonhardt, H. & Cardoso, M. C. DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters. Mol. Cell 10, 1355–1365 (2002).

    CAS  Article  Google Scholar 

  13. Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001).

    CAS  Article  Google Scholar 

  14. Bozhenok, L., Poot, R. A., Collins, N. & Varga-Weisz, P. in Methods in Enzymology Vol. 377 (eds Wu, C. & Allis, C. D.) 376–389 (Academic, San Diego, 2003).

    Google Scholar 

  15. Istomina, N. E. et al. Insulation of the chicken β-globin chromosomal domain from a chromatin-condensing protein, MENT. Mol. Cell. Biol. 23, 6455–6468 (2003).

    CAS  Article  Google Scholar 

  16. Grigoryev, S. A., Solovieva, V. O., Spirin, K. S. & Krasheninnikov, I. A. A novel nonhistone protein (MENT) promotes nuclear collapse at the terminal stage of avian erythropoiesis. Exp. Cell Res. 198, 268–275 (1992).

    CAS  Article  Google Scholar 

  17. Staynov, D. Z. & Proykova, Y. G. Quantitative analysis of DNase I digestion patterns of oligo- and polynucleosomes. J. Mol. Biol. 279, 59–71 (1998).

    CAS  Article  Google Scholar 

  18. Cusick, M. E., Lee, K. S., DePamphilis, M. L. & Wassarman, P. M. Structure of chromatin at deoxyribonucleic acid replication forks: nuclease hypersensitivity results from both prenucleosomal deoxyribonucleic acid and an immature chromatin structure. Biochemistry 22, 3873–3884 (1983).

    CAS  Article  Google Scholar 

  19. Martini, E., Roche, D. M., Marheineke, K., Verreault, A. & Almouzni, G. Recruitment of phosphorylated chromatin assembly factor 1 to chromatin after UV irradiation of human cells. J. Cell Biol. 143, 563–575 (1998).

    CAS  Article  Google Scholar 

  20. Lachner, M., O'Sullivan, R. J. & Jenuwein, T. An epigenetic road map for histone lysine methylation. J. Cell Sci. 116, 2117–2124 (2003).

    CAS  Article  Google Scholar 

  21. Sobel, R. E., Cook, R. G., Perry, C. A., Annunziato, A. T. & Allis, C. D. Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4. Proc. Natl Acad. Sci. USA 92, 1237–1241 (1995).

    CAS  Article  Google Scholar 

  22. Taddei, A., Roche, D., Sibarita, J. B., Turner, B. M. & Almouzni, G. Duplication and maintenance of heterochromatin domains. J. Cell Biol. 147, 1153–1166 (1999).

    CAS  Article  Google Scholar 

  23. Krude, T. Mimosine arrests proliferating human cells before onset of DNA replication in a dose-dependent manner. Exp. Cell Res. 247, 148–159 (1999).

    CAS  Article  Google Scholar 

  24. Henderson, D. S., Banga, S. S., Grigliatti, T. A. & Boyd, J. B. Mutagen sensitivity and suppression of position-effect variegation result from mutations in mus209, the Drosophila gene encoding PCNA. EMBO J. 13, 1450–1459 (1994).

    CAS  Article  Google Scholar 

  25. Zhang, Z., Shibahara, K. & Stillman, B. PCNA connects DNA replication to epigenetic inheritance in yeast. Nature 408, 221–225 (2000).

    CAS  Article  Google Scholar 

  26. Grewal, S. I. & Elgin, S. C. Heterochromatin: new possibilities for the inheritance of structure. Curr. Opin. Genet. Dev. 12, 178–187 (2002).

    CAS  Article  Google Scholar 

  27. Aagaard, L. et al. Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3–9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J. 18, 1923–1938 (1999).

    CAS  Article  Google Scholar 

  28. Ayyanathan, K. et al. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. Genes Dev. 17, 1855–1869 (2003).

    CAS  Article  Google Scholar 

  29. Minc, E., Courvalin, J. C. & Buendia, B. HP1γ associates with euchromatin and heterochromatin in mammalian nuclei and chromosomes. Cytogenet. Cell Genet. 90, 279–284 (2000).

    CAS  Article  Google Scholar 

  30. Gelbart, M. E., Rechsteiner, T., Richmond, T. J. & Tsukiyama, T. Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates. Mol. Cell. Biol. 21, 2098–2106 (2001).

    CAS  Article  Google Scholar 

  31. 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).

    CAS  Article  Google Scholar 

  32. Iida, T. & Araki, H. Noncompetitive counteractions of DNA polymerase ε and ISW2–yCHRAC for epigenetic inheritance of telomere position effect in Saccharomyces cerevisiae. Mol. Cell. Biol. 24, 217–227 (2004).

    CAS  Article  Google Scholar 

  33. 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 

  34. Dignam, J. D., Lebovitz, R. M. & Roeder, R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475–1489 (1983).

    CAS  Article  Google Scholar 

  35. 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 

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Acknowledgements

We thank W. Bickmore, A. Verreault, M. Bustin and R. Kingston for antibodies and reagents; R. Ferrer for a GST–PCNA construct; M. Rocchi for an α-satellite probe; T. Krude for advice on the use of mimosine; and G. Elliott for help with microscopy. Work in the laboratory of P.D.V.-W. is supported by the Marie Curie Cancer Care. D.v.d.B. was supported by grants from the Dutch Cancer Society (KWF), the British Council (Focus UK grant) and the Socrates exchange programme. Work in the laboratory of J.F. is supported by FCT-Portugal and FEDER (refs BCI-36194-99-00; SRFM-BPD-3547-2000), and by a Calouste Gulbenkian Foundation Award.

Author information

Author notes

  1. Raymond A. Poot & Ludmila Bozhenok

    Present address: MRC Clinical Sciences Centre, Imperial College School of Medicine, London, W12 0NN, UK

  2. Patrick D. Varga-Weisz

    Present address: Babraham Institute, Cambridge, CB2 4AT, UK

  3. Debbie L.C. van den Berg

    Present address: Center for Biomedical Genetics, Leiden University, 2300 AL, The Netherlands

  4. Raymond A. Poot, Ludmila Bozhenok and Debbie L.C. van den Berg: These authors contributed equally to this work.

Affiliations

  1. Marie Curie Research Institute, The Chart, Oxted, RH8 0TL, Surrey, UK

    Raymond A. Poot, Ludmila Bozhenok, Debbie L.C. van den Berg, Margaret Grimaldi & Patrick D. Varga-Weisz

  2. Institute of Molecular Medicine, Faculty of Medicine, Lisbon, 1649-028, Portugal

    Søren Steffensen, Fernando Ferreira & Joao Ferreira

  3. CIISA, Faculty of Veterinary Medicine, Lisbon, 1300-477, Portugal

    Fernando Ferreira

  4. MRC Human Genetics Unit, Edinburgh, EH4 2XU, UK

    Nick Gilbert

  5. Babraham Institute, Cambridge, CB2 4AT, UK

    Ludmila Bozhenok

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Correspondence to Patrick D. Varga-Weisz.

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Poot, R., Bozhenok, L., van den Berg, D. et al. The Williams syndrome transcription factor interacts with PCNA to target chromatin remodelling by ISWI to replication foci. Nat Cell Biol 6, 1236–1244 (2004). https://doi.org/10.1038/ncb1196

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