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

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

PROVIDER: PRJNA616370 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11453075.fastq.gz	Fastqsanger.gz
	SRR11453076.fastq.gz	Fastqsanger.gz
	SRR11453077.fastq.gz	Fastqsanger.gz
	SRR11453078.fastq.gz	Fastqsanger.gz
	SRR11453095_1.fastq.gz	Fastqsanger.gz

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

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

| PRJNA741903 | ENA

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]

| PRJNA616370 | ENA

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: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.

2024-05-01 | GSE263472 | 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

| PRJNA1097604 | ENA

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.

| S-EPMC10643137 | biostudies-literature

Selective chemical tracking of Dnmt1 catalytic activity in live cells

Project description:Selective chemical tracking of Dnmt1 catalytic activity in live cells

| PRJNA756279 | ENA

Live tracking of basal stem cells of the epidermis during growth, homeostasis, and injury response in zebrafish

Project description:Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self-renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self-renewal; however, this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single-cell tracking. Here, we report integrin b4 (itgb4) is a useful marker for basal cell labelling, irrespective of the body region, stage, and regenerative status. We employed Cre-loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells, including those in fins, became quiescent in the adult stage, genetic cell ablation showed that basal cells were reactivated to either self-renew or differentiate, depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals.

2023-09-06 | GSE241757 | GEO

Promoter Decommissioning by the NuRD Chromatin Remodeling Complex Triggers Synaptic Connectivity in the Mammalian Brain

Project description:Precise control of gene expression plays fundamental roles in brain development, but the roles of chromatin regulators in neuronal connectivity have remained poorly understood. Here, we find that depletion of the nucleosome remodeling and deacetylation (NuRD) complex in the cerebellar cortex by in vivo RNAi in rats and conditional knockout of the core NuRD subunit Chd4 in mice profoundly impairs the establishment of granule neuron parallel fiber/Purkinje cell synapses. In RNA-Seq analyses of Chd4 conditional knockout mice, we identify a set of nearly 200 genes that are repressed by the NuRD complex in the cerebellum in vivo. Genome-wide ChIP-Seq analyses reveal that the NuRD complex selectively decommissions the promoters of NuRD-repressed genes in the cerebellum in vivo by inducing the deacetylation of histone H3K9/14 and H3K27 and demethylation of H3K4 at these genes. Importantly, temporal control of promoter decommissioning and repression of NuRD target genes upon maturation of the cerebellum requires the NuRD complex. Finally, in a targeted in vivo RNAi screen of NuRD-repressed target genes, we identify the transcription factor Nhlh1, the RNA-binding protein Elavl2, and the presynaptic regulator Cplx3 as negative regulators of presynaptic differentiation in the cerebellar cortex. Together, these findings define NuRD-dependent promoter decommissioning as a developmentally regulated programming mechanism that releases the brake on presynaptic differentiation and thereby drives synaptic connectivity in the mammalian brain. Three distinct histone modifications using postnatal day 6 or day 22 cerebella from wild type (WT) or Chd4 conditional knockout (cKO) mice were examined in duplicate using libraries prepared with the Illumina ChIP-Seq DNA Sample Prep Kit and sequenced on the Illumina HiSeq 2000 platform.

2014-08-18 | E-GEOD-57758 | biostudies-arrayexpress

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