Regulation of chromatin microphase separation by binding of protein complexes

eLife, Journal Year: 2023, Volume and Issue: 12

Published: July 12, 2023

We show evidence of the association RNA polymerase II (RNAP) with chromatin in a core-shell organization, reminiscent microphase separation where cores comprise dense and shell, RNAP low density. These observations motivate our physical model for regulation organization. Here, we as multiblock copolymer, comprising active inactive regions (blocks) that are both poor solvent tend to be condensed absence binding proteins. However, quality can regulated by protein complexes (e.g., transcription factors). Using theory polymer brushes, find such leads swelling which turn modifies spatial organization regions. In addition, use simulations study spherical micelles, whose shells bound complexes. micelles increases number controls their size. Thus, genetic modifications affecting strength chromatin-binding may modulate experienced regulate genome.

Language: Английский

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Transcriptional condensates and phase separation: condensing information across scales and mechanisms

Nucleus, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 22, 2023

Transcription is the fundamental process of gene expression, which in eukaryotes occurs within complex physicochemical environment nucleus. Decades research have provided extreme detail molecular and functional mechanisms transcription, but spatial genomic organization transcription remains mysterious. Recent discoveries show that transcriptional components can undergo phase separation create distinct compartments inside nucleus, providing new models through to view eukaryotes. In this review, we focus on condensates their separation-like behaviors. We suggest differentiation between physical descriptions dynamic biomolecular assemblies required for productive discuss how are central organizing three-dimensional genome across temporal scales. Finally, map approaches therapeutic manipulation ask what technical advances needed understand more completely.

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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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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Chromatin structure and dynamics: one nucleosome at a time

Histochemistry and Cell Biology, Journal Year: 2024, Volume and Issue: 162(1-2), P. 79 - 90

Published: April 12, 2024

Language: Английский

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Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(22), P. 12573 - 12660

Published: Nov. 13, 2024

Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled study these signaling in living systems across temporal and spatial scales. Over years there has been an explosion number fluorescent biosensors, as they become available for numerous targets, utilized spectral space, suited various imaging techniques. To guide users this extensive biosensor landscape, we discuss critical aspects proteins consideration development, smart tagging strategies, historical recent types, grouped by target, with a focus on design applications sensors systems.

Language: Английский

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Expansion in situ genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 26, 2024

Microscopy and genomics are both used to characterize cell function, but approaches connect the two types of information lacking, particularly at subnuclear resolution. While emerging multiplexed imaging methods can simultaneously localize genomic regions nuclear proteins, their ability accurately measure DNA-protein interactions is constrained by diffraction limit optical microscopy. Here, we describe expansion in situ genome sequencing (ExIGS), a technology that enables DNA superresolution localization proteins single cells. We applied ExIGS fibroblast cells derived from an individual with Hutchinson-Gilford progeria syndrome how variation morphology affects spatial chromatin organization. Using this data, discovered lamin abnormalities linked hotspots aberrant euchromatin repression may erode identity. Further, show heterogeneously increase repressive environment nucleus tissues aged These results demonstrate serve as generalizable platform for connecting changes gene regulation across disease contexts.

Language: Английский

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Basic Epigenetic Mechanisms

Sub-cellular biochemistry/Subcellular biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 49

Published: Jan. 1, 2025

Language: Английский

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Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells

Science Advances, Journal Year: 2025, Volume and Issue: 11(13)

Published: March 28, 2025

A string of nucleosomes, where genomic DNA is wrapped around histones, organized in the cell as chromatin, ranging from euchromatin to heterochromatin, with distinct genome functions. Understanding physical differences between and heterochromatin crucial, yet specific labeling methods living cells remain limited. Here, we have developed replication-dependent histone (Repli-Histo) mark nucleosomes based on replication timing. Using this approach, investigated local nucleosome motion four known chromatin classes, human mouse cells. The more euchromatic (earlier-replicated) heterochromatic (later-replicated) regions exhibit greater lesser motions, respectively. Notably, profile each class persists throughout interphase. Genome essentially replicated although timing perturbed. Our findings, combined computational modeling, suggest that earlier-replicated accessibility, can be a major determinant genome-wide

Language: Английский

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The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization

Proceedings of the Japan Academy Series B, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The organization and dynamics of chromatin are critical for genome functions such as transcription DNA replication/repair. Historically, was assumed to fold into the 30-nm fiber progressively arrange larger helical structures, described in textbook model. However, over past 15 years, extensive evidence including our studies has dramatically transformed view from a static, regular structure one that is more variable dynamic. In higher eukaryotic cells, forms condensed yet liquid-like domains, which appear be basic unit structure, replacing fiber. These domains maintain proper accessibility, ensuring regulation reaction processes. During mitosis, these assemble form gel-like mitotic chromosomes, further constrained by condensins other factors. Based on available evidence, I discuss physical properties live emphasizing its viscoelastic nature-balancing local fluidity with global stability support functions.

Language: Английский

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