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Mechanism of DNA translocation underlying chromatin remodelling by Snf2

Author

Listed:
  • Meijing Li

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Advanced Innovation Center for Structural Biology)

  • Xian Xia

    (Tsinghua University
    Tsinghua University
    Beijing Advanced Innovation Center for Structural Biology)

  • Yuanyuan Tian

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Advanced Innovation Center for Structural Biology)

  • Qi Jia

    (Chinese Academy of Sciences)

  • Xiaoyu Liu

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Advanced Innovation Center for Structural Biology)

  • Ying Lu

    (Chinese Academy of Sciences)

  • Ming Li

    (Chinese Academy of Sciences)

  • Xueming Li

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Advanced Innovation Center for Structural Biology)

  • Zhucheng Chen

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Advanced Innovation Center for Structural Biology)

Abstract

Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme1,2. Among the remodelling enzymes, Snf2 serves as the prototype to study the action of this protein family. Snf2 and related enzymes share two conserved RecA-like lobes3, which by themselves are able to couple ATP hydrolysis to chromatin remodelling. The mechanism by which these enzymes couple ATP hydrolysis to translocate the nucleosome along the DNA remains unclear2,4–8. Here we report the structures of Saccharomyces cerevisiae Snf2 bound to the nucleosome in the presence of ADP and ADP-BeFx. Snf2 in the ADP-bound state adopts an open conformation similar to that in the apo state, and induces a one-base-pair DNA bulge at superhelix location 2 (SHL2), with the tracking strand showing greater distortion than the guide strand. The DNA distortion propagates to the proximal end, leading to staggered translocation of the two strands. The binding of ADP-BeFx triggers a closed conformation of the enzyme, resetting the nucleosome to a relaxed state. Snf2 shows altered interactions with the DNA in different nucleotide states, providing the structural basis for DNA translocation. Together, our findings suggest a fundamental mechanism for the DNA translocation that underlies chromatin remodelling.

Suggested Citation

  • Meijing Li & Xian Xia & Yuanyuan Tian & Qi Jia & Xiaoyu Liu & Ying Lu & Ming Li & Xueming Li & Zhucheng Chen, 2019. "Mechanism of DNA translocation underlying chromatin remodelling by Snf2," Nature, Nature, vol. 567(7748), pages 409-413, March.
  • Handle: RePEc:nat:nature:v:567:y:2019:i:7748:d:10.1038_s41586-019-1029-2
    DOI: 10.1038/s41586-019-1029-2
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    Citations

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    Cited by:

    1. Luka Bacic & Guillaume Gaullier & Jugal Mohapatra & Guanzhong Mao & Klaus Brackmann & Mikhail Panfilov & Glen Liszczak & Anton Sabantsev & Sebastian Deindl, 2024. "Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Li Wang & Jiali Yu & Zishuo Yu & Qianmin Wang & Wanjun Li & Yulei Ren & Zhenguo Chen & Shuang He & Yanhui Xu, 2022. "Structure of nucleosome-bound human PBAF complex," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Jiayi Fan & Andrew T. Moreno & Alexander S. Baier & Joseph J. Loparo & Craig L. Peterson, 2022. "H2A.Z deposition by SWR1C involves multiple ATP-dependent steps," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. 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.
    5. Chunli Yan & Thomas Dodd & Jina Yu & Bernice Leung & Jun Xu & Juntaek Oh & Dong Wang & Ivaylo Ivanov, 2021. "Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    6. Un Seng Chio & Eugene Palovcak & Anton A. A. Smith & Henriette Autzen & Elise N. Muñoz & Zanlin Yu & Feng Wang & David A. Agard & Jean-Paul Armache & Geeta J. Narlikar & Yifan Cheng, 2024. "Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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