ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one‑dimensional diffusion on DNA
- Johns Hopkins University, United States
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
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Data from: ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One-Dimensional Diffusion on DNADryad Digital Repository, doi:10.5061/dryad.ghx3ffbqw.
Article and author information
Author details
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.
Reviewing Editor
- Jerry L Workman, Stowers Institute for Medical Research, United States
Version history
- Received: January 25, 2022
- Preprint posted: January 26, 2022 (view preprint)
- Accepted: July 22, 2022
- Accepted Manuscript published: July 25, 2022 (version 1)
- Version of Record published: August 10, 2022 (version 2)
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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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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