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Cited by 4Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and FunctionGenomics and Chromatin Dynamics

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MagIC-Cryo-EM, structural determination on magnetic beads for scarce macromolecules in heterogeneous samples

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Arimura, Yasuhiro, Konishi, Hide A, Funabiki, Hironori·2025·eLife
DOI 10.7554/elife.103486.3PMC PMC10849486

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Abstract

Cryo-EM single-particle analyses typically require target macromolecule concentration at 0.05~5.0 mg/ml, which is often difficult to achieve. Here, we devise Ma g netic I solation and C oncentration (MagIC)-cryo-EM, a technique enabling direct structural analysis of targets captured on magnetic beads, thereby reducing the targets’ concentration requirement to <0.0005 mg/mL. Adapting MagIC-cryo-EM to a Chromatin Immunoprecipitation protocol, we characterized structural variations of the linker histone H1.8-associated nucleosomes that were isolated from interphase and metaphase chromosomes in Xenopus egg extract. Combining Du plicated S election T o E xclude R ubbish particles (DuSTER), a particle curation method that excludes low signal-to-noise ratio particles, we also resolved the 3D cryo-EM structures of nucleoplasmin NPM2 co-isolated with the linker histone H1.8 and revealed distinct open and closed structural variants. Our study demonstrates the utility of MagIC-cryo-EM for structural analysis of scarce macromolecules in heterogeneous samples and provides structural insights into the cell cycle-regulation of H1.8 association to nucleosomes.

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Metadata

Authors
Arimura, Y., Konishi, H. A., & Funabiki, H.
Affiliations
  • Fred Hutch Cancer Center (US)
  • Laboratory of Chromosome and Cell Biology, The Rockefeller University
  • Rockefeller University (US)
Corresponding author
  • Arimura, Yasuhiro
  • Funabiki, Hironori
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2025-05-20
Volume
13
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.103486.3
PMC
PMC10849486
OpenAlex
W4391103612
Cited by
4
References
2
Citations by year
2025: 1
FWCI
0.36
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
Funders
  • National Institute of General Medical Sciences (R35GM132111)
  • Japan Society for the Promotion of Science (Overseas Research Fellowships)
  • Osamu Hayaishi Memorial Scholarship (Scholarship for Study Abroad)
  • Stavros Niarchos Foundation (SNF Institute for Global Infectious Disease Research)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
magnetic bead isolation, nucleosome structure, chromatin immunoprecipitation, Xenopus egg extracts, cell cycle regulation

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