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. 2025:2919:91-107.
doi: 10.1007/978-1-0716-4486-7_6.

High-Resolution Cryo-EM Analyses of Nucleosomes

Yoshimasa Takizawa  1 , Cheng-Han Ho  1 , Shoko Sato  1 , Radostin Danev  2 , Hitoshi Kurumizaka  3   4
Affiliations

High-Resolution Cryo-EM Analyses of Nucleosomes

Yoshimasa Takizawa et al. Methods Mol Biol. 2025.

Abstract

The fundamental chromatin unit is the nucleosome, in which approximately 150 base pairs of DNA are bound to the surface of a symmetric histone octamer containing 2 copies each of histones H2A, H2B, H3, and H4. Over the years, numerous structures of nucleosomes have been determined by X-ray crystallography. However, their structural and functional versatility may not have been fully revealed, due to crystal packing effects. Various structures of nucleosomes and their complexes with nucleosome-binding proteins are now being determined by cryo-electron microscopy (cryo-EM) single-particle analysis, allowing the visualization of their structural diversity. In this report, we present a method for high-resolution structural analyses of nucleosomes by cryo-EM and describe the detailed procedures for nucleosome purification, cryo-EM grid preparation, data collection, and data processing. This method can serve as a good starting point for cryo-EM investigations of nucleosomes and their wide range of complexes.

Keywords: Chromatin; Cryo-EM; Nucleosome; Single-particle analysis.

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References

    1. Wolffe A (1998) Chromatin: structure and function, 3rd edn. Academic Press, San Diego
    1. Luger K, Dechassa ML, Tremethick DJ et al (2012) New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 13:436–447 - DOI - PubMed - PMC
    1. Venkatesh S, Workman JL (2015) Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol 16:178–189 - DOI - PubMed
    1. Luger K, Mäder AW, Richmond RK et al (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260 - DOI - PubMed
    1. Davey CA, Sargent DF, Luger K et al (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J Mol Biol 319:1097–1113 - DOI - PubMed

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