Evidence map›Paper›PMID 35881789›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2022

Stochastic particle unbinding modulates growth dynamics and size of transcription factor condensates in living cells.

Gorka Muñoz-Gil, Catalina Romero-Aristizabal, Nicolas Mateos, Felix Campelo, Lara I de Llobet Cucalon, Miguel Beato, Maciej Lewenstein, Maria F Garcia-Parajo, Juan A Torreno-Pina

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. Memory effects of transcription regulator-DNA interactions in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  6. Review
  7. Review
  8. Review
  9. Article
  10. Article
  11. Review
  12. Using single molecule imaging to explore intracellular heterogeneity.The international journal of biochemistry & cell biology · 2023
    Review
  13. Article
  14. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Gorka Muñoz-GilCFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain.
Catalina Romero-AristizabalCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
Nicolas MateosCFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain.ORCID 0000-0003-3272-2975
Felix CampeloCFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain.ORCID 0000-0002-0786-9548
Lara I de Llobet CucalonCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.ORCID 0000-0001-6249-7276
Miguel BeatoCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.ORCID 0000-0002-2878-2222
Maciej LewensteinCFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain.ORCID 0000-0002-0210-7800
Maria F Garcia-ParajoCFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain.ORCID 0000-0001-6618-3944
Juan A Torreno-PinaCFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain.ORCID 0000-0001-7314-3828

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Liquid-liquid phase separation (LLPS) is emerging as a key physical principle for biological organization inside living cells, forming condensates that play important regulatory roles. Inside living nuclei, transcription factor (TF) condensates regulate transcriptional initiation and amplify the transcriptional output of expressed genes. However, the biophysical parameters controlling TF condensation are still poorly understood. Here we applied a battery of single-molecule imaging, theory, and simulations to investigate the physical properties of TF condensates of the progesterone receptor (PR) in living cells. Analysis of individual PR trajectories at different ligand concentrations showed marked signatures of a ligand-tunable LLPS process. Using a machine learning architecture, we found that receptor diffusion within condensates follows fractional Brownian motion resulting from viscoelastic interactions with chromatin. Interestingly, condensate growth dynamics at shorter times is dominated by Brownian motion coalescence (BMC), followed by a growth plateau at longer timescales that result in nanoscale condensate sizes. To rationalize these observations, we extended on the BMC model by including the stochastic unbinding of particles within condensates. Our model reproduced the BMC behavior together with finite condensate sizes at the steady state, fully recapitulating our experimental data. Overall, our results are consistent with condensate growth dynamics being regulated by the escaping probability of PR molecules from condensates. The interplay between condensation assembly and molecular escaping maintains an optimum physical condensate size. Such phenomena must have implications for the biophysical regulation of other nuclear condensates and could also operate in multiple biological scenarios.

Indexed as

Biomolecular CondensatesCell NucleusReceptors, ProgesteroneSingle Molecule ImagingTranscription FactorsChromatinLigandsMachine LearningMotionChromatinLigandsReceptors, ProgesteroneTranscription Factorsbiomolecular condensatesBrownian motion coalescenceliquid–liquid phase separationsingle particle trackingtranscription factor

Identifiers

PMID35881789
PMCPMC9351496

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.