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Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1

Author

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  • Akihisa Osakabe

    (The University of Tokyo
    Japan Science and Technology Agency)

  • Yoshimasa Takizawa

    (The University of Tokyo)

  • Naoki Horikoshi

    (The University of Tokyo)

  • Suguru Hatazawa

    (The University of Tokyo)

  • Lumi Negishi

    (The University of Tokyo)

  • Shoko Sato

    (The University of Tokyo)

  • Frédéric Berger

    (Vienna Biocenter (VBC))

  • Tetsuji Kakutani

    (The University of Tokyo)

  • Hitoshi Kurumizaka

    (The University of Tokyo
    The University of Tokyo)

Abstract

The histone H2A variant H2A.W occupies transposons and thus prevents access to them in Arabidopsis thaliana. H2A.W is deposited by the chromatin remodeler DDM1, which also promotes the accessibility of chromatin writers to heterochromatin by an unknown mechanism. To shed light on this question, we solve the cryo-EM structures of nucleosomes containing H2A and H2A.W, and the DDM1-H2A.W nucleosome complex. These structures show that the DNA end flexibility of the H2A nucleosome is higher than that of the H2A.W nucleosome. In the DDM1-H2A.W nucleosome complex, DDM1 binds to the N-terminal tail of H4 and the nucleosomal DNA and increases the DNA end flexibility of H2A.W nucleosomes. Based on these biochemical and structural results, we propose that DDM1 counters the low accessibility caused by nucleosomes containing H2A.W to enable the maintenance of repressive epigenetic marks on transposons and prevent their activity.

Suggested Citation

  • Akihisa Osakabe & Yoshimasa Takizawa & Naoki Horikoshi & Suguru Hatazawa & Lumi Negishi & Shoko Sato & Frédéric Berger & Tetsuji Kakutani & Hitoshi Kurumizaka, 2024. "Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49465-w
    DOI: 10.1038/s41467-024-49465-w
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