Evidence map›Paper›PMID 41134621›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2025

Transcriptional condensates encode a "golden mean" to optimize enhancer-promoter communication across genomic distances.

Tao Zhu, Chunhe Li, Xiakun Chu

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Review
  2. Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Review
  3. Getting gene expression "just right".Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors.

Tao ZhuInstitute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China.ORCID 0009-0005-9616-9250
Chunhe LiInstitute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China.ORCID 0000-0002-9127-3930
Xiakun ChuAdvanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China.ORCID 0000-0003-3166-7070

Funding

Department of Education of Guangdong Province (DEGP) 2023KTSCX169GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province () 2024A1515010862| Guangdong Provincial Pearl River Talents Program () 2023QN10X037MOST | National Key Research and Development Program of China (NKPs) 2019YFA0709502MOST | National Natural Science Foundation of China (NSFC) 12171102MOST | National Natural Science Foundation of China (NSFC) 12474201MOST | National Natural Science Foundation of China (NSFC) 32201020
6 · The paper itself

Abstract

Enhancers regulate gene expression by physically contacting their target promoters, yet these contacts often span large genomic distances. Phase-separated condensates (droplet-like clusters) of transcription factors (TFs) are thought to facilitate such long-range enhancer-promoter (E-P) communication, but the quantitative principles underlying this mechanism remain unclear. Here, we use polymer-based chromatin simulations to systematically vary the strength of TF clustering and the E-P genomic distance, examining their combined effects on E-P contact formation. We find that E-P contact frequency shows a nonmonotonic dependence on the degree of TF clustering: Contact frequency peaks at an intermediate TF abundance and TF-TF affinity, leading to a "golden mean" optimum. Two distinct regimes emerge: Under weak TF-TF attraction, contact probability increases with condensate size, whereas strong TF attraction produces a peaked response that declines at high condensation levels. These results indicate that TF condensate acts as a tunable "rheostat," buffering E-P interactions against increasing genomic distances. However, excessive TF clustering leads to molecular crowding and competition that ultimately impair E-P communication. Our study, consistent with recent experiments, establishes a mechanistic framework at the molecular level, where balanced TF condensation enables robust long-range E-P communication, reconciling the stochastic nature of chromatin dynamics with the fidelity of gene regulation.

Indexed as

Enhancer Elements, GeneticPromoter Regions, GeneticTranscription FactorsTranscription, GeneticChromatinGene Expression RegulationModels, GeneticChromatinTranscription Factors4D genomecoarse-grained modelsphase separationstructure–dynamics–function relationshiptranscriptional cluster

Identifiers

PMID41134621
PMCPMC12582294

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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.