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

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. Wohlschlegel, Suhua Feng, Steve A. Kay, Z. Hong Zhou () and Steven E. Jacobsen ()
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Somsakul Pop Wongpalee: University of California, Los Angeles (UCLA)
Shiheng Liu: UCLA
Javier Gallego-Bartolomé: University of California, Los Angeles (UCLA)
Alexander Leitner: ETH Zürich
Ruedi Aebersold: ETH Zürich
Wanlu Liu: University of California, Los Angeles (UCLA)
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
Steven E. Jacobsen: University of California, Los Angeles (UCLA)

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-11759-9

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