ArticleBiophysical journal2022
Simulating the chromatin-mediated phase separation of model proteins with multiple domains.
Article in Biophysical journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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.
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.
Who cites it
19 citing papers in PubMed, 40 citations in OpenAlex.
- Mixing chromatin fibers with different nucleosome repeat lengths changes dynamics of chromatin phase separation.The Journal of biological chemistry · 2026Article
- Phase separation of ecDNA condensates establishes in-trans contact domains that boost selective MYC regulatory interactions.Nature communications · 2026Article
- Decoding the role of DNA sequence on protein-DNA co-condensation.PLoS computational biology · 2025Article
- Transcriptional condensates encode a "golden mean" to optimize enhancer-promoter communication across genomic distances.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multiphasic Organization and Differential Dynamics of Proteins within Protein-DNA Biomolecular Condensates.The journal of physical chemistry. B · 2025Article
- Protein-DNA co-condensation is prewetting to a collapsed polymer.Biophysical journal · 2025Article
- Differential oligomerization regulates PHF13 chromatin affinity and function.Nucleic acids research · 2025Article
- Article
- The Role of Lamins in Genome Organisation: A Modelling Perspective.Sub-cellular biochemistry · 2025Review
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning.Biophysical journal · 2024Article
- Chromatin and aberrant enhancer activity in KMT2A rearranged acute lymphoblastic leukemia.Current opinion in genetics & development · 2024Review
- The scales, mechanisms, and dynamics of the genome architecture.Science advances · 2024Review
- HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Biophysics of biomolecular condensates.Biophysical journal · 2023Article
- Detecting and quantifying liquid-liquid phase separation in living cells by model-free calibrated half-bleaching.Nature communications · 2022Article
- Computer simulations of chromatin phase separation.Biophysical journal · 2022Article
- RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins.PLoS computational biology · 2022Article
- Current Understanding of Molecular Phase Separation in Chromosomes.International journal of molecular sciences · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates that arise due to liquid-liquid phase separation, or a via a "bridging-induced attraction" mechanism. For proteins that interact multivalently, we obtain a phase diagram which includes liquid-like droplets, droplets with absorbed polymer, and coated polymer regimes. Of particular interest is a regime where protein droplets only form due to interaction with the polymer; here, unlike a standard phase separating system, droplet density rather than size varies with the overall protein concentration. We also observe that protein dynamics within droplets slow down as chromatin is absorbed. If the protein-protein interactions have a strictly limited valence, fractal or gel-like condensates are instead observed. A specific example that inspired our model is heterochromatin protein 1, or HP1. Recent in vivo experiments have shown that HP1 exhibits similar droplet size buffering behavior as our simulations. Overall, our results provide biologically relevant insights into the general nature of protein-chromatin condensates in living cells.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.