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

Peter H. Whitney,

Timothée Lionnet

Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 87, P. 102873 - 102873

Published: July 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.

Language: Английский

Sequence-dependent surface condensation of a pioneer transcription factor on DNA DOI Creative Commons
José A. Morín, Sina Wittmann, Sandeep Choubey

et al.

Nature Physics, Journal Year: 2022, Volume and Issue: 18(3), P. 271 - 276

Published: Feb. 3, 2022

Abstract Biomolecular condensates are dense assemblies of proteins that form distinct biochemical compartments without being surrounded by a membrane. Some, such as P granules and stress granules, behave droplets contain many millions molecules. Others, transcriptional on the surface DNA, small thousands The physics behind formation DNA surfaces is still under discussion. Here we investigate nature transcription factor using pioneer Krüppel-like 4 (Klf4). We show Klf4 can phase separate its own at high concentrations, but low only forms DNA. Using optical tweezers, demonstrate these type condensation. This condensation involves switch-like transition from thin adsorbed layer to thick condensed layer, which shows hallmarks prewetting transition. localization correlates with sequence, suggesting condensate sequence-dependent Prewetting together sequence specificity explain size position control condensates. speculate factors underlies positioning provides robustness regulation.

Language: Английский

Citations

123
RNA polymerase II dynamics shape enhancer–promoter interactions DOI
Gilad Barshad, James J. Lewis, Alexandra G. Chivu

et al.

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(8), P. 1370 - 1380

Published: July 10, 2023

Language: Английский

Citations

73
Transcriptional condensates: a blessing or a curse for gene regulation? DOI Creative Commons

Martín Stortz,

Diego M. Presman, Valeria Levi

et al.

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

Citations

26
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin DOI
Agnieszka Pancholi, Tim Klingberg, Weichun Zhang

et al.

Molecular Systems Biology, Journal Year: 2021, Volume and Issue: 17(9)

Published: Sept. 1, 2021

Language: Английский

Citations

64
Rheology and Viscoelasticity of Proteins and Nucleic Acids Condensates DOI Creative Commons
Davide Michieletto, Mattia Marenda

JACS Au, Journal Year: 2022, Volume and Issue: 2(7), P. 1506 - 1521

Published: June 13, 2022

Phase separation is as familiar watching vinegar separating from oil in vinaigrette. The observation that phase of proteins and nucleic acids widespread living cells has opened an entire field research into the biological significance biophysical mechanisms protein condensation biology. Recent evidence indicates certain condensates are not simple liquids instead display both viscous elastic behaviors, which turn may have significance. aim this Perspective to review state-of-the-art quickly emerging focusing on material rheological properties condensates. Finally, we discuss different techniques can be employed quantify viscoelasticity highlight potential future directions opportunities for interdisciplinary cross-talk between chemists, physicists, biologists.

Language: Английский

Citations

59
Mesoscale structure–function relationships in mitochondrial transcriptional condensates DOI Creative Commons
Marina Feric,

Azadeh Sarfallah,

Furqan Dar

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(41)

Published: Oct. 3, 2022

In live cells, phase separation is thought to organize macromolecules into membraneless structures known as biomolecular condensates. Here, we reconstituted transcription in condensates from purified mitochondrial components using optimized vitro reaction conditions probe the structure–function relationships of We find that core mt-transcription machinery form multiphasic, viscoelastic vitro. Strikingly, rates condensate-mediated are substantially lower than solution. The decrease transcriptional associated with formation vesicle-like driven by production and accumulation RNA during transcription. generation alters global behavior organization within Coarse-grained simulations mesoscale at equilibrium show stably assemble multiphasic vesicles formed result dynamical arrest. Overall, our findings illustrate complex transcribing, multicomponent condensates, they highlight intimate, bidirectional interplay structure function

Language: Английский

Citations

48
Regulation of chromatin microphase separation by binding of protein complexes DOI Creative Commons
Omar Adame-Arana, Gaurav Bajpai, Dana Lorber

et al.

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

Citations

25
HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation DOI Creative Commons
Maxime M. C. Tortora, Lucy D. Brennan, Gary H. Karpen

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(33)

Published: Aug. 7, 2023

The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid–liquid phase separation properties in vitro, its mechanistic impact on structure and dynamics PCH condensate formation vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate mutual coupling between self-interacting HP1-like molecules chromatin polymer. We reveal that specific affinity for H3K9me2/3 loci facilitates coacervation nucleo promotes stable condensates at levels far below concentration required observe purified protein assays vitro. These heterotypic HP1–chromatin interactions give rise strong dependence nucleoplasmic density HP1-H3K9me2/3 stoichiometry, consistent with thermodynamics multicomponent separation. dynamical cross talk viscoelastic scaffold also leads anomalously slow equilibration kinetics, which strongly depend distribution domains result coexistence multiple long-lived, microphase-separated compartments. morphology these complex coacervates is further found be governed by dynamic establishment underlying landscape, may drive their increasingly abnormal, aspherical shapes during cell development. findings compare favorably 4D microscopy measurements live Drosophila embryos suggest general quantitative model based interplay HP1-based polymer mechanics.

Language: Английский

Citations

25
Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair DOI Open Access
Emile Alghoul, Matteo Paloni, Arato Takedachi

et al.

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(10), P. 1640 - 1658.e9

Published: April 13, 2023

Language: Английский

Citations

24
Dynamic microenvironments shape nuclear organization and gene expression DOI Creative Commons
Gabriela Hayward-Lara, Matthew D. Fischer, Mustafa Mir

et al.

Current Opinion in Genetics & Development, Journal Year: 2024, Volume and Issue: 86, P. 102177 - 102177

Published: March 11, 2024

Language: Английский

Citations

11