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TitleResolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT.
Journal, issue, pagesMol Cell, Vol. 84, Issue 18, Page 3423-33437.e8, Year 2024
Publish dateSep 19, 2024
AuthorsMaik Engeholm / Johann J Roske / Elisa Oberbeckmann / Christian Dienemann / Michael Lidschreiber / Patrick Cramer / Lucas Farnung /
PubMed AbstractTo maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase ...To maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase II (RNAPII) generates hexasomes that occur directly adjacent to nucleosomes. The resulting hexasome-nucleosome complexes are then resolved by Chd1. We present two cryoelectron microscopy (cryo-EM) structures of Chd1 bound to a hexasome-nucleosome complex before and after restoration of the missing inner H2A/H2B dimer by FACT. Chd1 uniquely interacts with the complex, positioning its ATPase domain to shift the hexasome away from the nucleosome. In the absence of the inner H2A/H2B dimer, its DNA-binding domain (DBD) packs against the ATPase domain, suggesting an inhibited state. Restoration of the dimer by FACT triggers a rearrangement that displaces the DBD and stimulates Chd1 remodeling. Our results demonstrate how chromatin remodelers interact with a complex nucleosome assembly and suggest how Chd1 and FACT jointly support transcription by RNAPII.
External linksMol Cell / PubMed:39270644 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 6.85 Å
Structure data

51238

9gd0

EMDB-51238, PDB-9gd0:
Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-51239: Nucleosome portion of SHN103, unsharpened focused refinement.
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-51240: Hexasome portion of SHN103, unsharpened focused refinement.
Method: EM (single particle) / Resolution: 3.0 Å

51241

9gd1

EMDB-51241, PDB-9gd1:
Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-51242: Nucleosome portion of Chd1-bound SHN103, unsharpened focused refinement.
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-51243: Hexasome portion of Chd1-bound SHN103, unsharpened focused refinement.
Method: EM (single particle) / Resolution: 4.0 Å

51244

9gd2

EMDB-51244, PDB-9gd2:
Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp.
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-51245: Original nucleosome portion of DN103, unsharpened focused refinement
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-51246: Restored Chd1-bound nucleosome portion of DN103, unsharpened focused refinement
Method: EM (single particle) / Resolution: 4.2 Å

51247

9gd3

EMDB-51247, PDB-9gd3:
Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA.
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-51315: Unsharpened consensus map of hexasome-nucleosome complex SHN103
Method: EM (single particle) / Resolution: 4.25 Å

EMDB-51316: Unsharpened consensus map of hexasome-nucleosome complex SHN103 bound by Chd1
Method: EM (single particle) / Resolution: 4.9 Å

EMDB-51317: Unsharpened consensus map of dinucleosome DN103 bound by Chd1
Method: EM (single particle) / Resolution: 6.85 Å

Chemicals

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

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

Source
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsDNA BINDING PROTEIN / chromatin / remodeling / transcription / nucleosome

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