National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35GM132111
United States
Japan Society for the Promotion of Science (JSPS)
JSPS Overseas Research Fellowships
Japan
Citation
Journal: Mol Cell / Year: 2021 Title: Structural features of nucleosomes in interphase and metaphase chromosomes. Authors: Yasuhiro Arimura / Rochelle M Shih / Ruby Froom / Hironori Funabiki / 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- ...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.
History
Deposition
Apr 11, 2021
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Header (metadata) release
Sep 15, 2021
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Map release
Sep 15, 2021
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Update
Nov 17, 2021
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Current status
Nov 17, 2021
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10749 (Title: Closed linker DNA nucleosome reconstituted with GUB DNA Data size: 624.4 Data #1: GUB DNA nucleosome with "closed" linker DNA [micrographs - multiframe])
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