In diverse conditions, intrinsic chromatin condensates have liquid-like material properties

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(18)

Опубликована: Апрель 24, 2023

Nuclear DNA in eukaryotes is wrapped around histone proteins to form nucleosomes on a chromatin fiber. Dynamic folding of the fiber into loops and variations degree compaction regulate essential processes such as transcription, recombination, mitotic chromosome segregation. Our understanding physical properties that allow be dynamically remodeled even highly compacted states limited. Previously, we reported has an intrinsic capacity phase separate dynamic liquid-like condensates, which can regulated by cellular factors [B. A. Gibson et al. , Cell 179 470–484.e421 (2019)]. Recent contradictory reports claim specific set solution conditions required for fluidity condensates would otherwise solid [J. C. Hansen, K. Maeshima, M. J. Hendzel, Epigenetics Chromatin 14 50 (2021); H. Strickfaden 183 1772–1784.e1713 (2020)]. We sought resolve these discrepancies, our ability translate with confidence biophysical observations cells requires their precise characterization. Moreover, whether assemblies are or static affects how loop extrusion, remodeling will engage them inside cells. Here, show diverse without buffering components fragments separated fluids vitro. also explore sample preparation imaging affect experimental observation condensate dynamics. Last, describe vitro behaviors locally but globally constrained movement observed

Язык: Английский

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In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization

Nature Genetics, Год журнала: 2024, Номер 56(3), С. 483 - 492

Опубликована: Янв. 30, 2024

Abstract Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms driving the formation of these domains difficult to dissect in vivo and remain poorly understood. Here we reconstitute Saccharomyces cerevisiae vitro determine its 3D organization at subnucleosome resolution by micrococcal nuclease-based chromosome conformation capture dynamics simulations. We show that regularly spaced phased nucleosome arrays form resemble vivo. This demonstrates neither loop extrusion nor transcription is required for basic domain yeast. In addition, find boundaries reconstituted correspond nucleosome-free regions insulation strength scales with their width. Finally, compaction depends on linker length, longer linkers forming more compact structures. Together, our results demonstrate regular positioning important provide a proof-of-principle bottom-up genome studies.

Язык: Английский

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Boundary stacking interactions enable cross-TAD enhancer–promoter communication during limb development

Nature Genetics, Год журнала: 2024, Номер 56(2), С. 306 - 314

Опубликована: Янв. 18, 2024

Язык: Английский

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Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus

Science, Год журнала: 2025, Номер 387(6734)

Опубликована: Фев. 6, 2025

In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and spontaneous loading activity of components in absence coevolution. Using bacterial genomes integrated into Saccharomyces cerevisiae , which diverged from yeast more than 2 billion years ago, we show that nucleosomes, cohesins, associated transcriptional machinery can lead formation two different archetypes, one transcribed other silent, independently heterochromatin formation. These archetypes also form on eukaryotic exogenous sequences, depend composition, be predicted using neural networks trained native genome. They do not mix nucleus, leading a bipartite nuclear compartmentalization, reminiscent organization vertebrate nuclei.

Язык: Английский

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Physical Nature of Chromatin in the Nucleus

Cold Spring Harbor Perspectives in Biology, Год журнала: 2021, Номер 13(5), С. a040675 - a040675

Опубликована: Апрель 5, 2021

Kazuhiro Maeshima1,2, Shiori Iida1,2 and Sachiko Tamura1 1Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan 2Department School Life Science, Sokendai (Graduate University for Advanced Studies), Correspondence: kmaeshim{at}nig.ac.jp

Язык: Английский

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Crumpled Polymer with Loops Recapitulates Key Features of Chromosome Organization

Physical Review X, Год журнала: 2023, Номер 13(4)

Опубликована: Ноя. 13, 2023

Chromosomes are exceedingly long topologically-constrained polymers compacted in a cell nucleus. We recently suggested that chromosomes organized into loops by an active process of loop extrusion. Yet remain elusive to direct observations living cells; detection and characterization myriads such is major challenge. The lack tractable physical model polymer folded limits our ability interpret experimental data detect loops. Here, we introduce new - sequence loops, solve it analytically. Our simple geometrical argument show how affect statistics contacts across different scales, explaining universally observed shapes the contact probability. Moreover, reveal folding reduces density topological entanglements, novel phenomenon refer as "the dilution entanglements". Supported simulations this finding suggests up ~ 1 2Mb with not topologically constrained, yet become crumpled at larger scales. theoretical framework allows inference characteristics, draws picture chromosome organization, shows affects properties polymers.

Язык: Английский

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The role of loop extrusion in enhancer-mediated gene activation

Current Opinion in Genetics & Development, Год журнала: 2023, Номер 79, С. 102022 - 102022

Опубликована: Фев. 25, 2023

Gene expression patterns in complex multicellular organisms are regulated by enhancers, which communicate with their target gene promoters three-dimensional (3D) chromatin structures. Despite advances our understanding of the mechanisms that organize mammalian genomes into compartments and topologically associating domains (TADs), it is not well understood how specific interactions between enhancers controlled this 3D context. In review, we give an overview recent evidence shows a process loop extrusion plays important role regulation enhancer-promoter communication discuss insights molecular mechanism contributes to enhancer-mediated activation.

Язык: Английский

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Regulation of chromatin microphase separation by binding of protein complexes

eLife, Год журнала: 2023, Номер 12

Опубликована: Июль 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.

Язык: Английский

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Probe-free optical chromatin deformation and measurement of differential mechanical properties in the nucleus

eLife, Год журнала: 2024, Номер 13

Опубликована: Янв. 12, 2024

The nucleus is highly organized to facilitate coordinated gene transcription. Measuring the rheological properties of and its sub-compartments will be crucial understand principles underlying nuclear organization. Here, we show that strongly localized temperature gradients (approaching 1°C/µm) can lead substantial intra-nuclear chromatin displacements (>1 µm), while area lamina shape remain unaffected. Using particle image velocimetry (PIV), displacement fields calculated converted into spatio-temporally resolved maps various strain components. this approach, are reversible, indicating elastic contributions dominant in maintaining organization on time scale seconds. In genetically inverted nuclei, centrally compacted heterochromatin displays high resistance deformation, giving a rigid, solid-like appearance. Correlating spatially with fluorescent reporters conventional interphase nuclei reveals compartments possess distinct mechanical identities. Surprisingly, both densely loosely packed showed compared medium dense chromatin. Equally, nucleoli display particularly strong local anchoring heterochromatin. Our results establish how used drive out equilibrium obtain spatial their material responses.

Язык: 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, Год журнала: 2024, Номер 121(36)

Опубликована: Авг. 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.

Язык: Английский

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