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TitleMolecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.
Journal, issue, pagesNat Plants, Vol. 10, Issue 3, Page 374-380, Year 2024
Publish dateFeb 27, 2024
AuthorsYue Liu / Zhihui Zhang / Hongmiao Hu / Wei Chen / Fan Zhang / Qian Wang / Changshi Wang / Kaige Yan / Jiamu Du /
PubMed AbstractEukaryotic 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 linksNat Plants / PubMed:38413824
MethodsEM (single particle)
Resolution3.17 - 4.05 Å
Structure data

37529

8wh5

EMDB-37529, PDB-8wh5:
Structure of DDM1-nucleosome complex in the apo state
Method: EM (single particle) / Resolution: 3.58 Å

37533

8wh8

EMDB-37533, PDB-8wh8:
Structure of DDM1-nucleosome complex in ADP state
Method: EM (single particle) / Resolution: 3.6 Å

37535

8wh9

EMDB-37535, PDB-8wh9:
Structure of DDM1-nucleosome complex in ADP-BeFx state
Method: EM (single particle) / Resolution: 3.31 Å

37537

8wha

EMDB-37537, PDB-8wha:
Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Method: EM (single particle) / Resolution: 4.05 Å

37538

8whb

EMDB-37538, PDB-8whb:
Structure of nucleosome core particle of Arabidopsis thaliana
Method: EM (single particle) / Resolution: 3.17 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Source
  • arabidopsis thaliana (thale cress)
  • synthetic construct (others)
KeywordsGENE REGULATION / complex / nucleosome / chromatin remodeling / structural protein-hydrolase-dna complex / chromatin / histone / protein dna interaction / nucleoprotein

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