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Title | Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. |
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Journal, issue, pages | Nat Plants, Vol. 10, Issue 3, Page 374-380, Year 2024 |
Publish date | Feb 27, 2024 |
Authors | Yue Liu / Zhihui Zhang / Hongmiao Hu / Wei Chen / Fan Zhang / Qian Wang / Changshi Wang / Kaige Yan / Jiamu Du / |
PubMed Abstract | Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers. In plants, ...Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeF-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeF-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1. |
External links | Nat Plants / PubMed:38413824 |
Methods | EM (single particle) |
Resolution | 3.17 - 4.05 Å |
Structure data | EMDB-37529, PDB-8wh5: EMDB-37533, PDB-8wh8: EMDB-37535, PDB-8wh9: EMDB-37537, PDB-8wha: EMDB-37538, PDB-8whb: |
Chemicals | ChemComp-ADP: ChemComp-BEF: |
Source |
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Keywords | GENE REGULATION / complex / nucleosome / chromatin remodeling / structural protein-hydrolase-dna complex / chromatin / histone / protein dna interaction / nucleoprotein |