EMD-15172
H1-free palindromic nucleosome, state E
EMD-15172
Single-particle8.9 Å
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Map released: 14/12/2022
Last modified: 15/02/2023
Sample Organism:
Homo sapiens
Sample: 197-bp H1-free palindromic nucleosome
Deposition Authors: Alegrio Louro J
,
Beinsteiner B
,
Cheng TC,
Patel AKM
,
Boopathi R
,
Angelov D
,
Hamiche A
,
Bednar J
,
Kale S
,
Dimitrov S
,
Klaholz B
Sample: 197-bp H1-free palindromic nucleosome
Deposition Authors: Alegrio Louro J
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Nucleosome dyad determines the H1 C-terminus collapse on distinct DNA arms.
Louro JA
,
Boopathi R
,
Beinsteiner B
,
Mohideen Patel AK,
Cheng TC,
Angelov D
,
Hamiche A
,
Bendar J,
Kale S
,
Klaholz BP,
Dimitrov S
(2023) Structure , 31 , 201 - 212.e5
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(2023) Structure , 31 , 201 - 212.e5
Abstract:
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.
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.