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TitleNucleosome dyad determines the H1 C-terminus collapse on distinct DNA arms.
Journal, issue, pagesStructure, Vol. 31, Issue 2, Page 201-212.e5, Year 2023
Publish dateFeb 2, 2023
AuthorsJaime Alegrio Louro / Ramachandran Boopathi / Brice Beinsteiner / Abdul Kareem Mohideen Patel / Tat Cheung Cheng / Dimitar Angelov / Ali Hamiche / Jan Bendar / Seyit Kale / Bruno P Klaholz / Stefan Dimitrov /
PubMed AbstractNucleosomes are symmetric structures. However, binding of linker histones generates an inherently asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome ...Nucleosomes are symmetric structures. However, binding of linker histones generates an inherently asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome structure, and therefore also to chromatin, is unclear. Efforts to investigate potential asymmetry due to H1s have been hampered by the DNA sequence, which naturally differs in each gyre. To overcome this issue, we designed and analyzed by cryo-EM a nucleosome reconstituted with a palindromic (601L) 197-bp DNA. As in the non-palindromic 601 sequence, H1 restricts linker DNA flexibility but reveals partial asymmetrical unwrapping. However, in contrast to the non-palindromic nucleosome, in the palindromic nucleosome H1 CTD collapses to the proximal linker. Molecular dynamics simulations show that this could be dictated by a slightly tilted orientation of the globular domain (GD) of H1, which could be linked to the DNA sequence of the nucleosome dyad.
External linksStructure / PubMed:36610392
MethodsEM (single particle)
Resolution7.5 - 10.9 Å
Structure data

EMDB-15143: H1-bound palindromic nucleosome, state 4
Method: EM (single particle) / Resolution: 10.9 Å

EMDB-15144: H1-bound palindromic nucleosome, state 3
Method: EM (single particle) / Resolution: 9.6 Å

EMDB-15146: H1-bound palindromic nucleosome, state 2
Method: EM (single particle) / Resolution: 10.0 Å

EMDB-15147: H1-bound palindromic nucleosome, state 5
Method: EM (single particle) / Resolution: 10.4 Å

EMDB-15156: H1-bound palindromic nucleosome, state 6
Method: EM (single particle) / Resolution: 10.9 Å

EMDB-15168: H1-free palindromic nucleosome, state A
Method: EM (single particle) / Resolution: 8.3 Å

EMDB-15169: H1-free palindromic nucleosome, state B
Method: EM (single particle) / Resolution: 8.3 Å

EMDB-15170: H1-free palindromic nucleosome, state C
Method: EM (single particle) / Resolution: 7.5 Å

EMDB-15171: H1-free palindromic nucleosome, state D
Method: EM (single particle) / Resolution: 8.3 Å

EMDB-15172: H1-free palindromic nucleosome, state E
Method: EM (single particle) / Resolution: 8.9 Å

EMDB-15173: H1-free palindromic nucleosome, state F
Method: EM (single particle) / Resolution: 8.3 Å

15232

8aag

EMDB-15232, PDB-8aag:
H1-bound palindromic nucleosome, state 1
Method: EM (single particle) / Resolution: 10.0 Å

Source
  • homo sapiens (human)
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
KeywordsGENE REGULATION / linker histone H1 / nucleosome

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