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TitleStructural characterisation of chromatin remodelling intermediates supports linker DNA-dependent product inhibition as a mechanism for nucleosome spacing.
Journal, issue, pagesElife, Vol. 14, Year 2025
Publish dateDec 24, 2025
AuthorsAmanda L Hughes / Ramasubramanian Sundaramoorthy / Tom Owen-Hughes /
PubMed AbstractPreviously, we showed that Chd1 chromatin remodelling enzyme associates with nucleosomes oriented towards the longer linker (Sundaramoorthy et al., 2018) (1). Here, we report a series of structures ...Previously, we showed that Chd1 chromatin remodelling enzyme associates with nucleosomes oriented towards the longer linker (Sundaramoorthy et al., 2018) (1). Here, we report a series of structures of Chd1 bound to nucleosomes during ongoing ATP-dependent repositioning. Combining these with biochemical experiments and existing literature, we propose a model in which Chd1 first associates oriented to sample putative entry DNA. In an ATP-dependent reaction, the enzyme then redistributes to the opposite side of the nucleosome, where it subsequently adopts a conformation productive for DNA translocation. Once this active complex extends the nascent exit linker to approximately 15 bp, it is sensed by the Chd1 DNA binding domain, resulting in conversion to a product-inhibited state. These observations provide a mechanistic basis for the action of a molecular ruler element in nucleosome spacing.
External linksElife / PubMed:41439750 / PubMed Central
MethodsEM (single particle)
Resolution3.8 - 4.27 Å
Structure data

53590

9r5k

EMDB-53590, PDB-9r5k:
Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.
Method: EM (single particle) / Resolution: 4.2 Å

53595

9r5s

EMDB-53595, PDB-9r5s:
Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.
Method: EM (single particle) / Resolution: 3.8 Å

53596

9r5w

EMDB-53596, PDB-9r5w:
Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-53597: Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.
Method: EM (single particle) / Resolution: 4.27 Å

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • synthetic construct (others)
  • xenopus laevis (African clawed frog)
KeywordsGENE REGULATION / Nucleosome / Remodelling enzyme

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