ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA
Authors/Creators
- 1. Johns Hopkins Medicine
- 2. Johns Hopkins University
Description
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/s, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.
Notes
Please visit https://github.com/ccarcam1/SWR1_1D_Diffusion_Publication to download the Matlab scripts used to generate the main figures. The datasets provided are not in the raw .h5 file format since in the raw format the data is several hundreds of gigabytes, and is therefore not easily accessible. The provided datasets include raw kymograph information as well as the associated analysis of each kymograph (cropping, linear fitting, diffusion coefficients, etc.). Matlab version installed: R2021a
Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DGE-1746891
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: GM007445
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: S10 OD025221
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: R35 GM122569
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: R01 GM125831
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: T32 GM007445
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: F32 GM128299
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: F32 GM133151
Funding provided by: Howard Hughes Medical Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000011
Award Number:
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README_eLife_77352.txt
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Related works
- Is cited by
- 10.1101/2022.01.24.477290 (DOI)
- 10.7554/elife.77352 (DOI)
- Is derived from
- https://github.com/ccarcam1/SWR1_1D_Diffusion_Publication (URL)