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CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation

Author

Listed:
  • Yichen Zhong

    (University of Sydney)

  • Bishnu P. Paudel

    (University of Wollongong
    Illawarra Health and Medical Research Institute)

  • Daniel P. Ryan

    (The Australian National University)

  • Jason K. K. Low

    (University of Sydney)

  • Charlotte Franck

    (University of Sydney
    The University of Sydney)

  • Karishma Patel

    (University of Sydney)

  • Max J. Bedward

    (University of Sydney)

  • Mario Torrado

    (University of Sydney)

  • Richard J. Payne

    (The University of Sydney)

  • Antoine M. Oijen

    (University of Wollongong
    Illawarra Health and Medical Research Institute)

  • Joel P. Mackay

    (University of Sydney)

Abstract

Chromatin remodellers hydrolyse ATP to move nucleosomal DNA against histone octamers. The mechanism, however, is only partially resolved, and it is unclear if it is conserved among the four remodeller families. Here we use single-molecule assays to examine the mechanism of action of CHD4, which is part of the least well understood family. We demonstrate that the binding energy for CHD4-nucleosome complex formation—even in the absence of nucleotide—triggers significant conformational changes in DNA at the entry side, effectively priming the system for remodelling. During remodelling, flanking DNA enters the nucleosome in a continuous, gradual manner but exits in concerted 4–6 base-pair steps. This decoupling of entry- and exit-side translocation suggests that ATP-driven movement of entry-side DNA builds up strain inside the nucleosome that is subsequently released at the exit side by DNA expulsion. Based on our work and previous studies, we propose a mechanism for nucleosome sliding.

Suggested Citation

  • Yichen Zhong & Bishnu P. Paudel & Daniel P. Ryan & Jason K. K. Low & Charlotte Franck & Karishma Patel & Max J. Bedward & Mario Torrado & Richard J. Payne & Antoine M. Oijen & Joel P. Mackay, 2020. "CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15183-2
    DOI: 10.1038/s41467-020-15183-2
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    Cited by:

    1. Yichen Zhong & Hakimeh Moghaddas Sani & Bishnu P. Paudel & Jason K. K. Low & Ana P. G. Silva & Stefan Mueller & Chandrika Deshpande & Santosh Panjikar & Xavier J. Reid & Max J. Bedward & Antoine M. Oi, 2022. "The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

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