ArticleProceedings of the National Academy of Sciences of the United States of America2023
Polymer folding through active processes recreates features of genome organization.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed, 64 citations in OpenAlex.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Motorized chromosome models of mitotic chromosome folding.Nature communications · 2025Article
- Dynamics of microcompartment formation at the mitosis-to-G1 transition.Nature structural & molecular biology · 2025Article
- Behavior of Active Polymer Knots.Macromolecules · 2025Article
- Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction.bioRxiv : the preprint server for biology · 2025Article
- Article
- Protein-DNA co-condensation is prewetting to a collapsed polymer.Biophysical journal · 2025Article
- Giant activity-induced elasticity in entangled polymer solutions.Nature communications · 2025Article
- Bridging spatial and temporal scales of developmental gene regulation.Current opinion in genetics & development · 2025Review
- Article
- Neural network properties of hydrophilic polymers as a key for development of the general theory of evolution.Royal Society open science · 2025Review
- Rethinking chromatin accessibility: from compaction to dynamic interactions.Current opinion in genetics & development · 2025Review
- Article
- Transcriptional machinery as an architect of genome structure.Current opinion in structural biology · 2024Review
- Review
- An RNA-centric view of transcription and genome organization.Molecular cell · 2024Review
- Article
- Motorized chain models of the ideal chromosome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- The scales, mechanisms, and dynamics of the genome architecture.Science advances · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate. Moreover, chromatin motion varies with genomic coordinate, pointing toward a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers nonequilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward exploring whether active mechanisms contribute to shaping genome conformations, we discuss a data-driven approach.
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.