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

Science Advances, Год журнала: 2025, Номер 11(13)

Опубликована: Март 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

Язык: Английский

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

Science Advances, Год журнала: 2023, Номер 9(24)

Опубликована: Июнь 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.

Язык: 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, Год журнала: 2024, Номер 15(1)

Опубликована: Май 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.

Язык: Английский

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Chromatin structure and dynamics: one nucleosome at a time

Histochemistry and Cell Biology, Год журнала: 2024, Номер 162(1-2), С. 79 - 90

Опубликована: Апрель 12, 2024

Язык: Английский

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Transcription dynamics and genome organization in the mammalian nucleus: Recent advances

Molecular Cell, Год журнала: 2024, Номер unknown

Опубликована: Окт. 1, 2024

Язык: Английский

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The method in the madness: Transcriptional control from stochastic action at the single-molecule scale

Current Opinion in Structural Biology, Год журнала: 2024, Номер 87, С. 102873 - 102873

Опубликована: Июль 1, 2024

Cell states result from the ordered activation of gene expression by transcription factors. Transcription factors face opposing design constraints: they need to be dynamic trigger rapid cell state transitions, but also stable enough maintain terminal identities indefinitely. Recent progress in live-cell single-molecule microscopy has helped define biophysical principles underlying this paradox. Beyond factor activity, experiments have revealed that at nearly every level regulation, control emerges multiple short-lived stochastic interactions, rather than deterministic, interactions typical other biochemical pathways. This architecture generates consistent outcomes can rapidly choreographed. Here, we highlight recent results demonstrate how order regulation apparent molecular-scale chaos and discuss remaining conceptual challenges.

Язык: Английский

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Histone modifications of circulating nucleosomes are associated with changes in cell-free DNA fragmentation patterns

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(42)

Опубликована: Окт. 9, 2024

The analysis of tissues origin cell-free DNA (cfDNA) is research and diagnostic interest. Many studies focused on bisulfite treatment or immunoprecipitation protocols to assess the cfDNA. loss often occurs during such processes. Fragmentomics cfDNA molecules has uncovered a wealth information related There still much room for development tools assessing contributions from various into plasma using fragmentomic features. Hence, we developed an approach analyze relative different plasma, by identifying characteristic fragmentation patterns associated with selected histone modifications. We named this technique as FRAGmentomics-based Histone modification Analysis (FRAGHA). Deduced placenta-specific H3 lysine 27 acetylation (H3K27ac)-associated signal correlated well fetal fraction in maternal (Pearson’s r = 0.96). deduced liver-specific H3K27ac-associated donor-derived liver transplantation recipients 0.92) was significantly increased patients hepatocellular carcinoma (HCC) ( P < 0.01, Wilcoxon rank-sum test). Significant elevations erythroblasts-specific colon-specific signals were observed β-thalassemia major colorectal cancer, respectively. Furthermore, tissue-specific H3K27ac regions, machine learning algorithm enhance HCC detection, area under curve (AUC) up 0.97. Finally, genomic regions 4 trimethylation (H3K4me3) found exhibit This study shed light relationship between fragmentomics modifications, thus expanding armamentarium liquid biopsy.

Язык: Английский

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RNA polymerase II coordinates histone deacetylation at active promoters

Science Advances, Год журнала: 2025, Номер 11(6)

Опубликована: Фев. 5, 2025

Nucleosomes at promoters of active genes are marked by specific histone post-translational modifications and variants. These features thought to promote the formation maintenance an “open” chromatin environment that is suitable for transcription. However, recent reports have drawn conflicting conclusions about whether these depend on To further interrogate this relationship, we inhibited transcription initiation using triptolide, which triggered degradation RNA polymerase II, examined impact modifications. Transcription was not required either hormone-induced or steady-state start sites (TSSs) enhancers. Rather, blocking increased levels acetylation H2AZ incorporation TSSs. P300 activity dispensable effect, but inhibition deacetylases masked acetylation. Together, our results demonstrate occur independently Furthermore, findings suggest process coordinates removal limit gene activity.

Язык: Английский

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Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read sequencing

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Март 11, 2025

Abstract Faithful epigenetic inheritance across cell divisions is essential to maintaining identity and involves numerous modifications, whose roles in establishing chromatin architecture are less understood. Technological approaches temporally order modifications throughout the cycle often face limitations sequence resolution rely on potentially damaging mitotic labeling or conversion steps. Herein, we present M ethylation P seudotime A nalysis T hrough read-level H eterogeneity (MPATH), a label- conversion-free method infer post-replication DNA strand maturity from methylation patterns single molecules. We use MPATH hydroxymethylation inheritance, revealing that CpGs within cis-regulatory elements undergo transitions between states at sub-cell-cycle timescales. When applied long reads generated by NOMe-seq, uncovered relationships nucleosome occupancy maturity. Finally, extension of phased reveals allele-specific trends pseudotime distribution associated with X chromosome activity. Our findings suggest when coupled multimodal sequencing strategies, could provide valuable insights into restoration dynamics.

Язык: 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, Год журнала: 2025, Номер unknown

Опубликована: Янв. 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.

Язык: Английский

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