Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin

Kim, Jee Min; Visanpattanasin, Pat; Jou, Vivian; Liu, Sheng; Tang, Xiaona; Zheng, Qinsi; Li, Kai Yu; Snedeker, Jonathan C.; Lavis, Luke D.; Lionnet, Timothée; Wu, Carl

doi:10.7554/elife.69387

Cited by 59 publications

(62 citation statements)

References 112 publications

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“…Remodelers might interact on chromatin, as suggested by the trapping of wt BRM by the ATP-binding mutant BRM-K804R. Importantly, an accompanying report by Wu and colleagues, studying budding yeast remodelers through live-cell single molecule tracking, also revealed the key role of the ATPase in promoting dissociation from chromatin and fast remodeler kinetics ( Kim et al, 2021 ). Collectively, these in vivo results provide a framework for understanding remodeler function in genome regulation.…”

Section: Discussionmentioning

confidence: 99%

In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin

Tilly¹,

Chalkley²,

Knaap³

et al. 2021

eLife

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ATP-dependent chromatin remodelers control the accessibility of genomic DNA through nucleosome mobilization. However, the dynamics of genome exploration by remodelers, and the role of ATP hydrolysis in this process remain unclear. We used live-cell imaging of Drosophila polytene nuclei to monitor Brahma (BRM) remodeler interactions with its chromosomal targets. In parallel, we measured local chromatin condensation and its effect on BRM association. Surprisingly, only a small portion of BRM is bound to chromatin at any given time. BRM binds decondensed chromatin but is excluded from condensed chromatin, limiting its genomic search space. BRM-chromatin interactions are highly dynamic, whereas histone-exchange is limited and much slower. Intriguingly, loss of ATP hydrolysis enhanced chromatin retention and clustering of BRM, which was associated with reduced histone turnover. Thus, ATP hydrolysis couples nucleosome remodeling to remodeler release, driving a continuous transient probing of the genome.

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Section: Discussionmentioning

confidence: 99%

In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin

Tilly¹,

Chalkley²,

Knaap³

et al. 2021

eLife

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“…While the nucleosome depleted region is a region of open chromatin where accessibility to DNA is higher compared to DNA in gene bodies, SWR1 must compete with transcription factors and other DNA binding proteins for search on this DNA (Kim et al ., 2021; Kubik et al, 2019; Nguyen et al, 2021; Rhee and Pugh, 2012). Proteins that diffuse on DNA by 1D hopping are sometimes capable of bypassing protein barriers and nucleosomes (Gorman et al ., 2010; Hedglin and O’Brien, 2010).…”

Section: Resultsmentioning

confidence: 99%

“…Since only 7% of nucleosomes are targets of SWR1 histone exchange, we believe that +1 nucleosomes use their adjacent NDRs as antennas, promoting SWR1 binding and 1D search to encounter flanking nucleosomes (Mirny et al ., 2009). This increased efficiency in target localization through dimensional reduction of the search process may be one that could extend to other chromatin remodelers that act on nucleosomes adjacent to the NDR, such as RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 (Kim et al ., 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Facilitated diffusion has been shown to be essential for expediting the rate at which transcription factors and other DNA binding proteins can bind their target compared to a 3D search alone (Berg et al, 1981; Elf et al, 2007; Hannon et al, 1986; Ricchetti et al, 1988; Von Hippel and Berg, 1989). Furthermore, recently published in vivo single particle tracking found that chromatin remodelers have bound-state diffusion coefficients that are larger than that of bound H2B, hinting at the possibility that they may scan chromatin, but those studies could not distinguish between remodeler scanning and locally enhanced chromatin mobility (Kim et al, 2021; Ranjan et al, 2020). It is not known, however, if SWR1 or any other chromatin remodeler can linearly diffuse on DNA, and therefore make use of facilitated diffusion to expedite its target search process.…”

Section: Introductionmentioning

confidence: 99%

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ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One-Dimensional Diffusion on DNA

Carcamo

Poyton

Ranjan

et al. 2022

Preprint

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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 yeast chromatin remodeler that performs histone exchange on +1 nucleosomes which are adjacent to a nucleosome depleted region (NDR) at 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 cells.

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“…For example, chromatin loops and TAD boundary positioning can influence enhancer-promoter interactions and gene regulation (16)(17)(18). This multi-layered organization of 3D genome is not static: the chromatin fiber is semiflexible in nature and is also subjected to forces generated by ATP driven molecular machines along with thermal fluctuations (19)(20)(21). This leads to both spatial and temporal structural heterogeneity.…”

Section: Introductionmentioning

confidence: 99%

Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment

Das

Shen

McCord

2021

Preprint

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Inside the nucleus, chromosomes are subjected to direct physical interaction between different components, active forces, and thermal noise, leading to the formation of an ensemble of three-dimensional structures. However, it is still not well understood to what extent and how the structural ensemble varies from one chromosome region or cell-type to another. We designed a statistical analysis technique and applied it to single-cell chromosome imaging data to reveal the fluctuation of individual chromosome structures. By analyzing the resulting structural landscape, we find that the largest dynamic variation is the overall radius of gyration of the chromatin region, followed by domain reorganization within the region. By comparing different human cell-lines and experimental perturbations data using this statistical analysis technique and a network entropy approach, we identify both cell-type and condition-specific features of the structural landscapes. We identify a relationship between epigenetic state and the properties of chromosome structure fluctuation and validate this relationship through polymer simulations. Overall, our study suggests that the types of variation in a chromosome structure ensemble are cell-type as well as region-specific and can be attributed to constraints placed on the structure by factors such as variation in epigenetic state.

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Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin

Cited by 59 publications

References 112 publications

In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin

In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin

ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One-Dimensional Diffusion on DNA

Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment

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