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Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography

Author

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  • Meng Zhang

    (Lawrence Berkeley National Laboratory
    University of California
    University of California)

  • César Díaz-Celis

    (University of California
    University of California)

  • Jianfang Liu

    (Lawrence Berkeley National Laboratory)

  • Jinhui Tao

    (Pacific Northwest National Laboratory)

  • Paul D. Ashby

    (Lawrence Berkeley National Laboratory)

  • Carlos Bustamante

    (University of California
    University of California
    University of California
    University of California)

  • Gang Ren

    (Lawrence Berkeley National Laboratory)

Abstract

The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.

Suggested Citation

  • Meng Zhang & César Díaz-Celis & Jianfang Liu & Jinhui Tao & Paul D. Ashby & Carlos Bustamante & Gang Ren, 2024. "Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48305-1
    DOI: 10.1038/s41467-024-48305-1
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    References listed on IDEAS

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