Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4

Nature volume 446, pages 338–341 (2007)Cite this article

Abstract

CIA (CCG1-interacting factor A)/ASF1, which is the most conserved histone chaperone among the eukaryotes, was genetically identified as a factor for an anti-silencing function (Asf1)1 by yeast genetic screening. Shortly after that, the CIA–histone-H3–H4 complex was isolated from Drosophila as a histone chaperone CAF-1 stimulator2. Human CIA-I/II (ASF1a/b) was identified as a histone chaperone that interacts with the bromodomain—an acetylated-histone-recognizing domain—of CCG1, in the general transcription initiation factor TFIID3,4,5. Intensive studies have revealed that CIA/ASF1 mediates nucleosome assembly by forming a complex with another histone chaperone in human cells6 and yeast7, and is involved in DNA replication1,2, transcription4,8,9,10, DNA repair1,2,11,12 and silencing/anti-silencing1,2,8,13,14,15 in yeast. CIA/ASF1 was shown as a major storage chaperone for soluble histones in proliferating human cells6,16. Despite all these biochemical and biological functional analyses, the structure–function relationship of the nucleosome assembly/disassembly activity of CIA/ASF1 has remained elusive. Here we report the crystal structure, at 2.7 Å resolution, of CIA-I in complex with histones H3 and H4. The structure shows the histone H3–H4 dimer's mutually exclusive interactions with another histone H3–H4 dimer and CIA-I. The carboxy-terminal β-strand of histone H4 changes its partner from the β-strand in histone H2A to that of CIA-I through large conformational change. In vitro functional analysis demonstrated that CIA-I has a histone H3–H4 tetramer-disrupting activity. Mutants with weak histone H3–H4 dimer binding activity showed critical functional effects on cellular processes related to transcription. The histone H3–H4 tetramer-disrupting activity of CIA/ASF1 and the crystal structure of the CIA/ASF1–histone-H3–H4 dimer complex should give insights into mechanisms of both nucleosome assembly/disassembly and nucleosome semi-conservative replication.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Overall structure and biochemical analysis of the CIA-I – histone-H3 – H4 complex.
Figure 2: Physical and functional interaction between CIA and histone H3.
Figure 3: Physical and functional interaction between CIA and histone H4.

Similar content being viewed by others

References

  1. Le, S., Davis, C., Konopka, J. B. & Sternglanz, R. Two new S-phase-specific genes from Saccharomyces cerevisiae. Yeast 13, 1029–1042 (1997)

    Article  CAS  Google Scholar 

  2. Tyler, J. K. et al. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402, 555–560 (1999)

    Article  ADS  CAS  Google Scholar 

  3. Munakata, T., Adachi, N., Yokoyama, N., Kuzuhara, T. & Horikoshi, M. A human homologue of yeast anti-silencing factor has histone chaperone activity. Genes Cells 5, 221–233 (2000)

    Article  CAS  Google Scholar 

  4. Chimura, T., Kuzuhara, T. & Horikoshi, M. Identification and characterization of CIA/ASF1 as an interactor of bromodomains associated with TFIID. Proc. Natl Acad. Sci. USA 99, 9334–9339 (2002)

    Article  ADS  CAS  Google Scholar 

  5. Umehara, T. & Horikoshi, M. Transcription initiation factor IID-interactive histone chaperone CIA-II implicated in mammalian spermatogenesis. J. Biol. Chem. 278, 35660–35667 (2003)

    Article  CAS  Google Scholar 

  6. Tagami, H., Ray-Gallet, D., Almouzni, G. & Nakatani, Y. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116, 51–61 (2004)

    Article  CAS  Google Scholar 

  7. Green, E. M. et al. Replication-independent histone deposition by the HIR complex and Asf1. Curr. Biol. 15, 2044–2049 (2005)

    Article  CAS  Google Scholar 

  8. Sharp, J. A., Fouts, E. T., Krawitz, D. C. & Kaufman, P. D. Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing. Curr. Biol. 11, 463–473 (2001)

    Article  CAS  Google Scholar 

  9. Adkins, M. W., Howar, S. R. & Tyler, J. K. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol. Cell 14, 657–666 (2004)

    Article  CAS  Google Scholar 

  10. Schwabish, M. A. & Struhl, K. Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol. Cell 22, 415–422 (2006)

    Article  CAS  Google Scholar 

  11. Emili, A., Schieltz, D. M., Yates, J. R. & Hartwell, L. H. Dynamic interaction of DNA damage checkpoint protein Rad53 with chromatin assembly factor Asf1. Mol. Cell 7, 13–20 (2001)

    Article  CAS  Google Scholar 

  12. Hu, F., Alcasabas, A. & Elledge, A. J. Asf1 links Rad53 to control of chromatin assembly. Genes Dev. 15, 1061–1066 (2001)

    Article  CAS  Google Scholar 

  13. Osada, S. et al. The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev. 15, 3155–3168 (2001)

    Article  CAS  Google Scholar 

  14. Meijsing, S. H. & Ehrenhofer-Murray, A. E. The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev. 15, 3169–3182 (2001)

    Article  CAS  Google Scholar 

  15. Umehara, T., Chimura, T., Ichikawa, N. & Horikoshi, M. Polyanionic stretch-deleted histone chaperone cia1/Asf1p is functional both in vivo and in vitro. Genes Cells 7, 59–73 (2002)

    Article  CAS  Google Scholar 

  16. Groth, A. et al. Human Asf1 regulates the flow of S phase histones during replicational stress. Mol. Cell 17, 301–311 (2005)

    Article  CAS  Google Scholar 

  17. Sillje, H. H. & Nigg, E. A. Identification of human Asf1 chromatin assembly factors as substrates of Tousled-like kinases. Curr. Biol. 11, 1068–1073 (2001)

    Article  CAS  Google Scholar 

  18. English, C. M., Maluf, N. K., Tripet, B., Churchill, M. E. & Tyler, J. K. ASF1 binds to a heterodimer of histones H3 and H4: a two-step mechanism for the assembly of the H3–H4 heterotetramer on DNA. Biochemistry 44, 13673–13682 (2005)

    Article  CAS  Google Scholar 

  19. Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41–45 (2000)

    Article  ADS  CAS  Google Scholar 

  20. Cosgrove, M. S., Boeke, J. D. & Wolberger, C. Regulated nucleosome mobility and the histone code. Nature Struct. Mol. Biol. 11, 1037–1043 (2004)

    Article  CAS  Google Scholar 

  21. Luger, K., Mäder, 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)

    Article  ADS  CAS  Google Scholar 

  22. Mousson, F. et al. Structural basis for the interaction of Asf1 with histone H3 and its functional implications. Proc. Natl Acad. Sci. USA 102, 5975–5980 (2005)

    Article  ADS  CAS  Google Scholar 

  23. Silverman, S. J. & Fink, G. R. Effects of Ty insertions on HIS4 transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 4, 1246–1251 (1984)

    Article  CAS  Google Scholar 

  24. Yamaguchi, Y., Narita, T., Inukai, N., Wada, T. & Handa, H. SPT genes: key players in the regulation of transcription, chromatin structure and other cellular processes. J. Biochem. 129, 185–191 (2001)

    Article  CAS  Google Scholar 

  25. Matsubara, K., Sano, N., Umehara, T. & Horikoshi, M. Global analysis of functional surfaces of core histones with comprehensive point mutants. Genes Cells 12, 13–33 (2007)

    Article  CAS  Google Scholar 

  26. Collaborative computational project number 4. CCP4 suite: Programs for protein crystallography by collaborative computational project number 4. Acta Crystallogr. D. 50, 760–763 (1994)

  27. Abramoff, M. D., Magelhaes, P. J. & Ram, S. J. Image processing with ImageJ. Biophotonics International 11, 36–42 (2004)

    Google Scholar 

  28. Tang, Y. et al. Structure of a human ASF1–HIRA complex and insights into specificity of histone chaperone complex assembly. Nature Struct. Mol. Biol. 13, 921–929 (2006)

    Article  CAS  Google Scholar 

  29. DeLano, W. L. The PyMOL Molecular Graphics System 〈http://www.pymol.org〉 (2006)

  30. English, C. M., Adkins, M. W., Carson, J. J., Churchill, M. E. & Tyler, J. K. Structure basis of the histone chaperone activity of Asf1. Cell 127, 495–508 (2006)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank T. K. Kundu for the expression vector of Xenopus histones; F. Winston for yeast strains; K. Matsubara, Y. Ikejiri, S. Okano and S. Yoshihara for the construction of the histone mutants; and K. Hasegawa for critical reading of the manuscript. This study was supported in part by the New Energy and Industrial Technology Development Organization (NEDO) of Japan, the Exploratory Research for Advanced Technology (ERATO) of the Japan Science and Technology Agency (JST), and Ministry of Education, Culture, Sports, Science and Technology of Japan.

Author Contributions R.N. and M.E. contributed equally to this work. R.N. and Y.A. performed crystallographic and biochemical works. M.E. and N.S. performed biochemical works and yeast genetics. T.S. performed crystallographic work. M.H. and T.S. contributed to the idea, strategy, project management and writing of the manuscript. All authors discussed the results and commented on the manuscript.

The atomic coordinates have been deposited in the Protein Data Bank (PDB code, 2IO5).

Author information

Author notes

  1. Ryo Natsume and Masamitsu Eitoku: These authors contributed equally to this work.

Authors and Affiliations

  1. Japan Biological Information Research Centre (JBIRC), Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan,

    Ryo Natsume & Yusuke Akai

  2. Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan,

    Masamitsu Eitoku, Norihiko Sano & Masami Horikoshi

  3. Horikoshi Gene Selector Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), 5-9-6 Tokodai, Tsukuba, Ibaraki 300-2635, Japan,

    Masami Horikoshi

  4. Biological Information Research Centre (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan,

    Toshiya Senda

Authors
  1. Ryo Natsume
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masamitsu Eitoku
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yusuke Akai
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Norihiko Sano
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Masami Horikoshi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Toshiya Senda
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Masami Horikoshi or Toshiya Senda.

Ethics declarations

Competing interests

The atomic coordinates have been deposited in the Protein Data Bank (PDB code, 2IO5). Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-9 with Legends, Supplementary Methods, Supplementary Tables 1-3, and additional references. (PDF 2148 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Natsume, R., Eitoku, M., Akai, Y. et al. Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4. Nature 446, 338–341 (2007). https://doi.org/10.1038/nature05613

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature05613

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing