Transcriptional condensates: a blessing or a curse for gene regulation?

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Feb. 16, 2024

Whether phase-separation is involved in the organization of transcriptional machinery and if it aids or inhibits process a matter intense debate. In this Mini Review, we will cover current knowledge regarding role condensates on gene expression regulation. We summarize latest discoveries relationship between condensate formation, genome organization, activity, focusing strengths weaknesses experimental approaches used to interrogate these aspects transcription living cells. Finally, discuss challenges for future research.

Language: Английский

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Mature chromatin packing domains persist after RAD21 depletion in 3D

Science Advances, Journal Year: 2025, Volume and Issue: 11(4)

Published: Jan. 24, 2025

Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin essential for TAD loop features in Hi-C, but the corresponding change structure has not been studied using electron microscopy. Pairing scanning transmission tomography with multiomic analysis single-molecule localization microscopy, we study role regulating conformationally defined nanoscopic packing domains. Our results indicate domains are manifestation TADs. Using found only 20% lost upon RAD21 depletion. The effect depletion restricted to small, poorly packed (nascent) In addition, present evidence cohesin-mediated extrusion generates nascent undergo maturation through nucleosome posttranslational modifications. demonstrate a 3D genomic structure, composed domains, generated activity

Language: Английский

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Is euchromatin really open in the cell?

Trends in Cell Biology, Journal Year: 2023, Volume and Issue: 34(1), P. 7 - 17

Published: June 27, 2023

Language: Английский

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Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states

Science Advances, Journal Year: 2023, Volume and Issue: 9(24)

Published: June 14, 2023

How chromatin dynamics relate to transcriptional activity remains poorly understood. Using single-molecule tracking, coupled with machine learning, we show that histone H2B and multiple chromatin-bound regulators display two distinct low-mobility states. Ligand activation results in a marked increase the propensity of steroid receptors bind lowest-mobility state. Mutational analysis revealed interactions state require an intact DNA binding domain oligomerization domains. These states are not spatially separated as previously believed, but individual bound-TF molecules can dynamically switch between them on time scales seconds. Single different mobilities exhibit dwell distributions, suggesting mobility TFs is intimately their dynamics. Together, our identify unique appear represent common pathways for transcription mammalian cells.

Language: Английский

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Transcription-induced active forces suppress chromatin motion

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(12)

Published: March 15, 2024

The organization of interphase chromosomes in a number species is starting to emerge thanks advances variety experimental techniques. However, much less known about the dynamics, especially functional states chromatin. Some experiments have shown that motility individual loci human chromosome decreases during transcription and increases upon inhibiting transcription. This counterintuitive finding because it thought active mechanical force (

Language: Английский

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Orientation-independent-DIC imaging reveals that a transient rise in depletion attraction contributes to mitotic chromosome condensation

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(36)

Published: Aug. 27, 2024

Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in assembly of chromosomes, physical bases condensation process remain unclear. Depletion attraction/macromolecular crowding, an effective attractive force that arises between large structures crowded environments around may contribute to process. approach this issue, we investigated “chromosome milieu” mitosis living human using orientation-independent-differential interference contrast module combined with a confocal laser scanning microscope, which capable precisely mapping optical path differences estimating molecular densities. We found density surrounding chromosomes increased progression from prophase anaphase, concurring chromosome condensation. However, went down telophase, when decondensation began. Changes by hypotonic or hypertonic treatment consistently altered levels In vitro, native was converted liquid droplets presence cations macromolecular crowder. Additional crowder made stiffer more solid-like. These results suggest transient rise depletion attraction, likely triggered relocation macromolecules (proteins, RNAs, others) via nuclear envelope breakdown subsequent decrease cell volumes, contributes condensation, shedding light on different aspect mechanism cells.

Language: Английский

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Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 16, 2024

Abstract In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform simultaneously visualize single protein dynamics together with local chromatin environment in live cells. Together super-resolution imaging, new fluorescent probes, biophysical modeling, demonstrate nucleosomes display differential diffusion packing arrangements as density increases whereas viscoelastic properties accessibility interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive manner is dependent both on relative location within nucleus. Our results support model wherein transcription locally stabilizes while allowing for free exchange proteins. Additionally, they reveal heterogeneity arises from active passive highlight need account different organizational principles when modeling environments.

Language: Английский

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Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 21, 2024

Abstract In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this relationship, considering chromatin-chromatin interactions, modifications, extrusion. predict that heterochromatic governed by balance among diffusive flux methylated histones sustaining them acetylation reactions in process loop extrusion via supercoiling RNAPII at their periphery, which contributes to reduction. Super-resolution nano-imaging five distinct cell lines confirm predictions indicating absence leads larger heterochromatin domains. Furthermore, accurately reproduces findings regarding how transcription-mediated loss can mitigate impacts excessive cohesin loading. Our shed light role genome organization, offering insights into dynamics potential therapeutic targets.

Language: Английский

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Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 25, 2024

Abstract Although our understanding of the involvement heterochromatin architectural factors in shaping nuclear organization is improving, there still ongoing debate regarding role active genes this process. In study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate relationship between gene transcription and 3D folding. Our analysis uncovers a nonmonotonic - globally positive correlation intragenic contact density Pol II occupancy, independent cohesin-based loop extrusion. Through development biophysical model integrating dynamics within polymer chromosome organization, demonstrate that II-mediated attractive interactions with limited valency transcribed regions yield quantitative predictions consistent chromosome-conformation-capture live-imaging experiments. work provides compelling evidence transcriptional activity shapes 4D genome through micro-compartmentalization.

Language: Английский

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Single-nucleosome imaging unveils that condensins and nucleosome–nucleosome interactions differentially constrain chromatin to organize mitotic chromosomes

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 21, 2024

For accurate mitotic cell division, replicated chromatin must be assembled into chromosomes and faithfully segregated daughter cells. While protein factors like condensin play key roles in this process, it is unclear how chromosome assembly proceeds as molecular events of nucleosomes living cells condensins act on to organize chromosomes. To approach these questions, we investigate nucleosome behavior during mitosis human using single-nucleosome tracking, combined with rapid-protein depletion technology computational modeling. Our results show that local motion becomes increasingly constrained assembly, which functionally distinct from condensed apoptotic chromatin. Condensins crosslinkers, locally constraining Additionally, nucleosome-nucleosome interactions via histone tails constrain compact whole findings elucidate the physical nature process mitosis.

Language: Английский

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