ArticleBiophysical journal2020
The Interplay between Phase Separation and Gene-Enhancer Communication: A Theoretical Study.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Phase separation of ecDNA condensates establishes in-trans contact domains that boost selective MYC regulatory interactions.Nature communications · 2026Article
- Formation of topologically associated chromatin domains using quantum annealing.Scientific reports · 2026Article
- A Self-Organized Liquid Reaction Container for Cellular Memory.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- 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
- Differential oligomerization regulates PHF13 chromatin affinity and function.Nucleic acids research · 2025Article
- The cancer-associated fibroblast facilitates YAP liquid-liquid phase separation to promote cancer cell stemness in HCC.Cell communication and signaling : CCS · 2025Article
- Polymer models of chromatin organization in virally infected cells.Biochemical Society transactions · 2025Review
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells.Nature communications · 2024Article
- Article
- Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling.International journal of molecular sciences · 2023Review
- Computer simulations of chromatin phase separation.Biophysical journal · 2022Article
- Review
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- BET inhibition disrupts transcription but retains enhancer-promoter contact.Nature communications · 2021Article
- Chromosomes Phase Transition to Function.Biophysical journal · 2020Article
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3 authors.
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Abstract
The phase separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is investigated here. This is achieved by means of extensive molecular dynamics simulations of a simple polymer model that includes regulatory proteins as interacting spherical particles. Our interest is particularly focused on the role played by phase separation in the formation of molecule aggregates that can join distant regulatory elements, such as gene promoters and enhancers, along the DNA. We find that the overall equilibrium state of the system resulting from the mutual interplay between binding molecules and chromatin can lead, under suitable conditions that depend on molecules concentration, molecule-molecule, and molecule-DNA interactions, to the formation of phase-separated molecular clusters, allowing robust contacts between regulatory sites. Vice versa, the presence of regulatory sites can promote the phase-separation process. Different dynamical regimes can generate the enhancer-promoter contact, either by cluster nucleation at binding sites or by bulk spontaneous formation of the mediating cluster to which binding sites are successively attracted. The possibility that such processes can explain experimental live-cell imaging data measuring distances between regulatory sites during time is also discussed.
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