Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

Science, Journal Year: 2022, Volume and Issue: 376(6592), P. 496 - 501

Published: April 14, 2022

Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF loop-extruding cohesins, but the live dynamics of loop formation stability remain unknown. Here, we directly visualized chromatin looping at

Language: Английский

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Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(12), P. 1919 - 1932

Published: Dec. 1, 2022

It remains unclear why acute depletion of CTCF (CCCTC-binding factor) and cohesin only marginally affects expression most genes despite substantially perturbing three-dimensional (3D) genome folding at the level domains structural loops. To address this conundrum, we used high-resolution Micro-C nascent transcript profiling in mouse embryonic stem cells. We find that enhancer-promoter (E-P) interactions are largely insensitive to (3-h) CTCF, or WAPL. YY1 has been proposed as a regulator E-P loops, but also had minimal effects on transcription 3D folding. Strikingly, live-cell, single-molecule imaging revealed reduced factor (TF) binding chromatin. Thus, although cohesin, WAPL is not required for short-term maintenance gene expression, our results suggest may facilitate TFs search bind their targets more efficiently.

Language: Английский

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Cohesin and CTCF control the dynamics of chromosome folding

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(12), P. 1907 - 1918

Published: Dec. 1, 2022

In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, long they last and depend on the dynamics chromosome folding loop extrusion activity cohesin. By imaging chromosomal locations at high spatial temporal resolution in living cells, we show that are transient occur during course a cell cycle. Interactions become more frequent longer presence convergent CTCF sites, resulting suppression variability time. Supported by physical models dynamics, our data suggest CTCF-anchored loops around 10 min. Our results long-range transcriptional regulation might rely proximity, cohesin stabilize highly dynamic structures, facilitating selected subsets interactions.

Language: Английский

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Transcription shapes 3D chromatin organization by interacting with loop extrusion

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(11)

Published: March 10, 2023

Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. "Loop extrusion" can be impeded chromatin-bound factors, such as CTCF, which generates characteristic and functional organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin active promoters are loading sites. However, effects of on have not reconciled observations extrusion cohesin. To determine how modulates extrusion, we studied mouse cells in could alter abundance, dynamics, localization genetic "knockouts" regulators CTCF Wapl. Through Hi-C experiments, discovered intricate, cohesin-dependent contact patterns near genes. Chromatin around genes exhibited hallmarks interactions between transcribing RNA polymerases (RNAPs) cohesins. These reproduced polymer simulations RNAPs were moving barriers to obstructed, slowed, pushed The predicted preferential at is inconsistent our experimental data. Additional ChIP-seq experiments showed putative loader Nipbl predominantly enriched promoters. Therefore, propose preferentially loaded barrier function RNAP accounts for accumulation Altogether, find an stationary, but rather, translocates Loop might interact dynamically generate maintain gene regulatory elements shape genomic organization.

Language: Английский

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Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(6), P. 1048 - 1056

Published: May 8, 2023

Language: Английский

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The spatial organization of transcriptional control

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 24(1), P. 53 - 68

Published: Sept. 14, 2022

Language: Английский

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Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(5), P. 832 - 840

Published: April 3, 2023

Language: Английский

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CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion

Nature, Journal Year: 2023, Volume and Issue: 616(7958), P. 822 - 827

Published: April 19, 2023

Abstract In eukaryotes, genomic DNA is extruded into loops by cohesin 1 . By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs) 2,3 that have important roles in gene regulation and recombination during development disease 1,4–7 How CTCF establishes TAD boundaries to what extent these are permeable unclear 8 Here, address questions, we visualize interactions of single molecules on vitro. We show sufficient block diffusing cohesin, possibly reflecting how cohesive accumulates at boundaries, also loop-extruding boundaries. functions asymmetrically, as predicted; however, dependent tension. Moreover, regulates cohesin’s loop-extrusion activity changing its direction inducing loop shrinkage. Our data indicate not, previously assumed, simply a barrier cohesin-mediated extrusion but an active regulator whereby permeability can be modulated These results reveal mechanistic principles controls genome architecture.

Language: Английский

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The Smc5/6 complex is a DNA loop-extruding motor

Nature, Journal Year: 2023, Volume and Issue: 616(7958), P. 843 - 848

Published: April 19, 2023

Structural maintenance of chromosomes (SMC) protein complexes are essential for the spatial organization chromosomes1. Whereas cohesin and condensin organize by extrusion DNA loops, molecular functions third eukaryotic SMC complex, Smc5/6, remain largely unknown2. Using single-molecule imaging, we show that Smc5/6 forms loops extrusion. Upon ATP hydrolysis, reels symmetrically into at a force-dependent rate one kilobase pair per second. extrudes in form dimers, whereas monomeric unidirectionally translocates along DNA. We also find subunits Nse5 Nse6 (Nse5/6) act as negative regulators loop Nse5/6 inhibits loop-extrusion initiation hindering dimerization but has no influence on ongoing Our findings reveal level establish conserved mechanism among complexes.

Language: Английский

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3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

Cell Reports, Journal Year: 2023, Volume and Issue: 42(4), P. 112068 - 112068

Published: April 1, 2023

The spatiotemporal control of gene expression is dependent on the activity cis-acting regulatory sequences, called enhancers, which regulate target genes over variable genomic distances and, often, by skipping intermediate promoters, suggesting mechanisms that enhancer-promoter communication. Recent genomics and imaging technologies have revealed highly complex interaction networks, whereas advanced functional studies started interrogating forces behind physical communication among multiple enhancers promoters. In this review, we first summarize our current understanding factors involved in communication, with a particular focus recent papers new layers complexities to old questions. second part subset connected "hubs" discuss their potential functions signal integration regulation, as well putative might determine dynamics assembly.

Language: Английский

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