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CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation

Author

Listed:
  • Somsakul Pop Wongpalee

    (University of California, Los Angeles (UCLA)
    Chiang Mai University)

  • Shiheng Liu

    (UCLA
    California NanoSystems Institute (CNSI), UCLA)

  • Javier Gallego-Bartolomé

    (University of California, Los Angeles (UCLA))

  • Alexander Leitner

    (ETH Zürich)

  • Ruedi Aebersold

    (ETH Zürich
    University of Zürich)

  • Wanlu Liu

    (University of California, Los Angeles (UCLA)
    Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine)

  • Linda Yen

    (University of California, Los Angeles (UCLA))

  • Maria A. Nohales

    (University of Southern California)

  • Peggy Hsuanyu Kuo

    (University of California, Los Angeles (UCLA))

  • Ajay A. Vashisht

    (UCLA)

  • James A. Wohlschlegel

    (UCLA)

  • Suhua Feng

    (University of California, Los Angeles (UCLA))

  • Steve A. Kay

    (University of Southern California)

  • Z. Hong Zhou

    (UCLA
    California NanoSystems Institute (CNSI), UCLA)

  • Steven E. Jacobsen

    (University of California, Los Angeles (UCLA)
    UCLA)

Abstract

Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components of the DDR complex DRD1, DMS3 and RDM1, but the assembly process of this complex and the underlying mechanism for Pol V recruitment remain unknown. Here we show that all DDR complex components co-localize with Pol V, and we report the cryoEM structures of two complexes associated with Pol V recruitment—DR (DMS3-RDM1) and DDR′ (DMS3-RDM1-DRD1 peptide), at 3.6 Å and 3.5 Å resolution, respectively. RDM1 dimerization at the center frames the assembly of the entire complex and mediates interactions between DMS3 and DRD1 with a stoichiometry of 1 DRD1:4 DMS3:2 RDM1. DRD1 binding to the DR complex induces a drastic movement of a DMS3 coiled-coil helix bundle. We hypothesize that both complexes are functional intermediates that mediate Pol V recruitment.

Suggested Citation

  • Somsakul Pop Wongpalee & Shiheng Liu & Javier Gallego-Bartolomé & Alexander Leitner & Ruedi Aebersold & Wanlu Liu & Linda Yen & Maria A. Nohales & Peggy Hsuanyu Kuo & Ajay A. Vashisht & James A. Wohls, 2019. "CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-11759-9
    DOI: 10.1038/s41467-019-11759-9
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    Cited by:

    1. Zheng Li & Ming Wang & Zhenhui Zhong & Javier Gallego-Bartolomé & Suhua Feng & Yasaman Jami-Alahmadi & Xinyi Wang & James Wohlschlegel & Sylvain Bischof & Jeff A. Long & Steven E. Jacobsen, 2023. "The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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