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TitleMechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures.
Journal, issue, pagesStructure, Year 2024
Publish dateMay 31, 2024
AuthorsHongwei Zhang / Zhanxi Gu / Yuan Zeng / Yu Zhang /
PubMed AbstractThe SWI/SNF2 chromatin remodeling factor decreased DNA methylation 1 (DDM1) is essential for the silencing of transposable elements (TEs) in both euchromatic and heterochromatic regions. Here, we ...The SWI/SNF2 chromatin remodeling factor decreased DNA methylation 1 (DDM1) is essential for the silencing of transposable elements (TEs) in both euchromatic and heterochromatic regions. Here, we determined the cryo-EM structures of DDM1-nucleosome and DDM1-nucleosome complexes at near-atomic resolution in the presence of the ATP analog ADP-BeFx. The structures show that nucleosomal DNA is unwrapped more on the surface of the histone octamer containing histone H2A than that containing histone H2A.W. DDM1 embraces one DNA gyre of the nucleosome and interacts with the N-terminal tails of histone H4. Although we did not observe DDM1-H2A.W interactions in our structures, the results of the pull-down experiments suggest a direct interaction between DDM1 and the core region of histone H2A.W. Our work provides mechanistic insights into the heterochromatin remodeling process driven by DDM1 in plants.
External linksStructure / PubMed:38870940
MethodsEM (single particle)
Resolution3.1 - 3.17 Å
Structure data

37098

8kcb

EMDB-37098, PDB-8kcb:
Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2
Method: EM (single particle) / Resolution: 3.17 Å

37099

8kcc

EMDB-37099, PDB-8kcc:
Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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

Source
  • arabidopsis thaliana (thale cress)
  • synthetic construct (others)
KeywordsSTRUCTURAL PROTEIN / DDM1 / nucleosome / H2A / H2A.W

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