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

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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.

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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.

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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).

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Correspondence to Masami Horikoshi or Toshiya Senda.

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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.

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Supplementary Information

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

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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) doi:10.1038/nature05613

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