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Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

ABSTRACT: Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

PROVIDER: PRJNA741903 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14929843_1.fastq.gz	Fastqsanger.gz
	SRR14929843_2.fastq.gz	Fastqsanger.gz
	SRR14929844_1.fastq.gz	Fastqsanger.gz
	SRR14929844_2.fastq.gz	Fastqsanger.gz
	SRR14929845_1.fastq.gz	Fastqsanger.gz

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Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Project description:Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex. The NuRD complex binds to all active enhancers to modulate transcription and here we use Hi-C experiments to show that it blurs TAD boundaries and increases the proximity of intermediate-range (~1 Mb) genomic sequences and enhancer-promoter interactions. To understand whether NuRD alters the dynamics of 3D genome structure, we developed an approach to segment and extract key biophysical parameters from 3D single-molecule trajectories of the NuRD complex determined using live-cell imaging. Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure and makes NuRD-bound enhancers move faster, increasing the overall volume of the nucleus that these key regulatory regions explore. Interestingly, we also uncovered a rare fast-diffusing state of NuRD bound enhancers that exhibits directed motion. The NuRD complex reduces the amount of time that enhancers remain in this fast-diffusing state, which we propose might otherwise re-organise enhancer-promoter proximity.

2023-05-31 | GSE179007 | GEO

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer/promoter dynamics [ChIP-seq]

Project description:Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer/promoter dynamics [ChIP-seq]

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Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer/promoter dynamics [ChIP-seq]

Project description:Enhancer-promoter dynamics are critical for the spatiotemporal control of gene expression, but it remains unclear how these dynamics are controlled by the nucleosome remodelling and deacetylase (NuRD) complex that is found at nearly all active enhancers and promoters. We show that MBD3-dependent assembly of the intact NuRD complex increases CTCF/Cohesin binding (using ChIP-seq) and the probability of the interaction of intermediate-range (~1Mb) genomic sequences (using population Hi-C). Using single-molecule imaging, we then revealed that these changes are related to how the chromatin moves, and that the intact NuRD complex increases how fast the nucleus is explored by NuRD-bound enhancers and promoters.

2021-04-01 | GSE147789 | GEO

Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions

Project description:Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions

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Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions

Project description:Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression. Here, we extended live-cell single-molecule tracking studies in fission yeast to determine how HP1 proteins interact with their binding partners in the nucleus. We measured how genetic perturbations that affect H3K9me alter the diffusive properties of HP1 proteins and each of their binding partners based on which we inferred their most likely interaction sites. Our results indicate that H3K9me promotes specific complex formation between HP1 proteins and their interactors in a spatially restricted manner, while attenuating their ability to form off-chromatin complexes. As opposed to being an inert platform or scaffold to direct HP1 binding, our studies propose a novel function for H3K9me as an active participant in enhancing HP1-associated complex formation in living cells.

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Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD.

Project description:To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer-promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds to chromatin for minutes, decompacts chromatin structure and increases enhancer dynamics. We also uncovered a rare fast-diffusing state of enhancers and found that NuRD restricts the time spent in this state. Hi-C and Cut&Run experiments revealed that NuRD modulates enhancer-promoter interactions in active chromatin, allowing them to contact each other over longer distances. Furthermore, NuRD leads to a marked redistribution of CTCF and, in particular, cohesin. We propose that NuRD promotes a decondensed chromatin environment, where enhancers and promoters can contact each other over longer distances, and where the resetting of enhancer-promoter interactions brought about by the fast decondensed chromatin motions is reduced, leading to more stable, long-lived enhancer-promoter relationships.

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2023-09-06 | GSE241757 | GEO

Dimerization of iLID optogenetic proteins observed using 3D single-molecule tracking in live E. coli.

Project description:3D single-molecule tracking microscopy has enabled measurements of protein diffusion in living cells, offering information about protein dynamics and cellular environments. For example, different diffusive states can be resolved and assigned to protein complexes of different size and composition. However, substantial statistical power and biological validation, often through genetic deletion of binding partners, are required to support diffusive state assignments. When investigating cellular processes, real-time perturbations to protein spatial distributions is preferable to permanent genetic deletion of an essential protein. For example, optogenetic dimerization systems can be used to manipulate protein spatial distributions that could offer a means to deplete specific diffusive states observed in single-molecule tracking experiments. Here, we evaluate the performance of the iLID optogenetic system in living E. coli cells using diffraction-limited microscopy and 3D single-molecule tracking. We observed a robust optogenetic response in protein spatial distributions after 488 nm laser activation. Surprisingly, 3D single-molecule tracking results indicate activation of the optogenetic response when illuminating with high-intensity light with wavelengths at which there is minimal photon absorbance by the LOV2 domain. The preactivation can be minimized through the use of iLID system mutants, and titration of protein expression levels.

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