1. Chromosomes and Gene Expression
  2. Structural Biology and Molecular Biophysics

ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one‑dimensional diffusion on DNA

  1. Claudia C Carcamo
  2. Matthew F Poyton
  3. Anand Ranjan
  4. Giho Park
  5. Robert K Louder
  6. Xinyu A Feng
  7. Jee Min Kim
  8. Thuc Dzu
  9. Carl Wu  Is a corresponding author
  10. Taekjip Ha  Is a corresponding author
  1. Johns Hopkins University, United States
https://doi.org/10.7554/eLife.77352
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Cite this article
  1. Claudia C Carcamo
  2. Matthew F Poyton
  3. Anand Ranjan
  4. Giho Park
  5. Robert K Louder
  6. Xinyu A Feng
  7. Jee Min Kim
  8. Thuc Dzu
  9. Carl Wu
  10. Taekjip Ha
(2022)
ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one‑dimensional diffusion on DNA
eLife 11:e77352.
https://doi.org/10.7554/eLife.77352
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Abstract

One-dimensional (1D) target search is a well-characterized phenomenon for many DNA binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a conserved yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome-depleted region (NDR) at gene promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single-particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 μm2/sec, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.

Data availability

Raw data has been uploaded to Dryad in the form of a Matlab structured arrays. All Matlab codes used to generate the main figures are publicly available athttps://github.com/ccarcam1/SWR1_1D_Diffusion_Publication

The following data sets were generated

Article and author information

Author details

  1. Claudia C Carcamo

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2646-188X

  2. Matthew F Poyton

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1261-2138

  3. Anand Ranjan

    Department of Biology, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6071-6017

  4. Giho Park

    Department of Biology, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Robert K Louder

    Department of Biology, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Xinyu A Feng

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Jee Min Kim

    Department of Biology, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Thuc Dzu

    Department of Biology, Johns Hopkins University, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Carl Wu

    Department of Biology, Johns Hopkins University, Baltimore, United States
    For correspondence
    wuc@jhu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6933-5763

  10. Taekjip Ha

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
    For correspondence
    tjha@jhu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2195-6258

Funding

National Institutes of Health (S10 OD025221)

  • Taekjip Ha

Howard Hughes Medical Institute

  • Taekjip Ha

National Institutes of Health (R35 GM122569)

  • Taekjip Ha

National Institutes of Health (R01 GM125831)

  • Carl Wu

National Science Foundation (DGE-1746891)

  • Claudia C Carcamo

National Institutes of Health (T32 GM007445)

  • Claudia C Carcamo

National Institutes of Health (F32 GM128299)

  • Matthew F Poyton

National Institutes of Health (F32 GM133151)

  • Robert K Louder

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2022, Carcamo et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Claudia C Carcamo
  2. Matthew F Poyton
  3. Anand Ranjan
  4. Giho Park
  5. Robert K Louder
  6. Xinyu A Feng
  7. Jee Min Kim
  8. Thuc Dzu
  9. Carl Wu
  10. Taekjip Ha
(2022)
ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one‑dimensional diffusion on DNA
eLife 11:e77352.
https://doi.org/10.7554/eLife.77352

Share this article

https://doi.org/10.7554/eLife.77352

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