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Cited by 59Genomics and Chromatin DynamicsNuclear Structure and FunctionAdvanced Electron Microscopy Techniques and Applications

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Structural features of nucleosomes in interphase and metaphase chromosomes

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Arimura, Yasuhiro, Shih, Rochelle M., Froom, Ruby, Funabiki, Hironori·2021·Molecular Cell
DOI 10.1016/j.molcel.2021.08.010PMC PMC8571072

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Abstract

Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.

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Metadata

Authors
Arimura, Y., Shih, R. M., Froom, R., & Funabiki, H.
Affiliations
Rockefeller University (US)
Corresponding author
  • Arimura, Yasuhiro
  • Funabiki, Hironori
ORCID
Venue
Molecular Cell
Publisher
Elsevier BV
Published
2021-11
Volume
81
Issue
21
Pages
4377-4397.e12
ISSN
1097-2765 (ISSN-L)
DOI
10.1016/j.molcel.2021.08.010
PMC
PMC8571072
OpenAlex
W3196371936
Cited by
59
References
2
Citations by year
2026: 12 · 2025: 16 · 2024: 9 · 2023: 7 · 2022: 12 · 2021: 3
FWCI
2.43
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Cell (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Japan Society for the Promotion of Science
  • National Institutes of Health (R35GM132111)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
Keywords
nucleosome structure, interphase chromosomes, metaphase chromosomes, chromatin structure, linker DNA, chromatosome, DNA supercoiling, cell cycle, post-translational modification, cryo-EM structure determination
MeSH terms
Protein Domains, Animals, Cell Communication, Cell Cycle, Cell Division, Chromatin, Chromosomes, Computer Simulation, DNA, Humans, Interphase, Metaphase, Nucleosomes, Protein Conformation, Protein Processing, Post-Translational, Xenopus, Cryoelectron Microscopy, Hydrophobic and Hydrophilic Interactions

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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