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Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails

Author

Listed:
  • Yunhui Peng

    (National Institutes of Health)

  • Shuxiang Li

    (Queen’s University)

  • Alexey Onufriev

    (Physics Department
    Computer Science Department
    Center for Soft Matter and Biological Physics)

  • David Landsman

    (National Institutes of Health)

  • Anna R. Panchenko

    (Queen’s University)

Abstract

Little is known about the roles of histone tails in modulating nucleosomal DNA accessibility and its recognition by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full nucleosome, totaling 65 microseconds of molecular dynamics simulations. We observe rapid conformational transitions between tail bound and unbound states, and characterize kinetic and thermodynamic properties of histone tail-DNA interactions. Different histone types exhibit distinct binding modes to specific DNA regions. Using a comprehensive set of experimental nucleosome complexes, we find that the majority of them target mutually exclusive regions with histone tails on nucleosomal/linker DNA around the super-helical locations ± 1, ± 2, and ± 7, and histone tails H3 and H4 contribute most to this process. These findings are explained within competitive binding and tail displacement models. Finally, we demonstrate the crosstalk between different histone tail post-translational modifications and mutations; those which change charge, suppress tail-DNA interactions and enhance histone tail dynamics and DNA accessibility.

Suggested Citation

  • Yunhui Peng & Shuxiang Li & Alexey Onufriev & David Landsman & Anna R. Panchenko, 2021. "Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25568-6
    DOI: 10.1038/s41467-021-25568-6
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    Cited by:

    1. Shuxiang Li & Tiejun Wei & Anna R. Panchenko, 2023. "Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

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