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TitleCryo-EM Structures of Native Chromatin Units From Human Cells.
Journal, issue, pagesGenes Cells, Vol. 30, Issue 3, Page e70019, Year 2025
Publish dateApr 14, 2025
AuthorsSuguru Hatazawa / Yoshiyuki Fukuda / Yuki Kobayashi / Lumi Negishi / Masahide Kikkawa / Yoshimasa Takizawa / Hitoshi Kurumizaka /
PubMed AbstractIn eukaryotic cells, genomic DNA is compacted by nucleosomes, as basic repeating units, into chromatin. The nucleosome arrangement in chromatin fibers could be an important determinant for chromatin ...In eukaryotic cells, genomic DNA is compacted by nucleosomes, as basic repeating units, into chromatin. The nucleosome arrangement in chromatin fibers could be an important determinant for chromatin folding, by which genomic DNA is regulated in the nucleus. To study the structures of chromatin units in cells, we have established a method for the structural analysis of native mono- and poly-nucleosomes prepared from HeLa cells. In this method, the chromatin in isolated nuclei was crosslinked to preserve the proximity information between nucleosomes, followed by chromatin fragmentation by micrococcal nuclease treatment. The mono- and poly-nucleosomes were then fractionated by sucrose gradient ultracentrifugation, and their structures were analyzed by cryo-electron microscopy. Cryo-electron microscopy single particle analysis and cryo-electron tomography visualized a native nucleosome structure and secondary nucleosome arrangements in cellular chromatin. This method provides a complementary strategy to fill the gap between in vitro and in situ analyses of chromatin structure.
External linksGenes Cells / PubMed:40223781 / PubMed Central
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution3.1 - 16.0 Å
Structure data

EMDB-63078: Cryo-EM structure of the native HeLa nucleosome
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-63079: Cryo-EM structure of the native HeLa nucleosome in poly-nucleosomes (class 1)
Method: EM (single particle) / Resolution: 4.09 Å

EMDB-63080: Cryo-EM structure of the native HeLa nucleosome in poly-nucleosomes (class 2)
Method: EM (single particle) / Resolution: 3.89 Å

EMDB-63081: Cryo-EM structure of the native HeLa nucleosome in poly-nucleosomes (class 3)
Method: EM (single particle) / Resolution: 3.64 Å

EMDB-63144: Subtomogram average of the HeLa nucleosome
Method: EM (subtomogram averaging) / Resolution: 14.9 Å

EMDB-63145: Subtomogram average of the HeLa nucleosome for mapping back
Method: EM (subtomogram averaging) / Resolution: 16.0 Å

Source
  • Homo sapiens (human)

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