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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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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.

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