ArticleMolecular cell2018
Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci.
Article in Molecular cell, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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Who cites it
97 citing papers in PubMed, 206 citations in OpenAlex.
- A scaffolding element rewires local 3D chromatin architecture during differentiation.Nature communications · 2026Article
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- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- The physical chemistry of interphase loop extrusion.Cell genomics · 2026Article
- TF-loop: deciphering the transcription factor regulatory language for CTCF-mediated chromatin loop based on BERT.Briefings in bioinformatics · 2026Article
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Chromatin unfolding via loops can drive clustered transposon insertion.Biophysical journal · 2025Article
- Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription.Physical review letters · 2025Article
- Role of RNA in genome folding: It's all about affinity.Current opinion in structural biology · 2025Review
- Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.Biophysical journal · 2025Article
- Differential oligomerization regulates PHF13 chromatin affinity and function.Nucleic acids research · 2025Article
- Bridging spatial and temporal scales of developmental gene regulation.Current opinion in genetics & development · 2025Review
- A Multiscale Perspective on Chromatin Architecture through Polymer Physics.Physiology (Bethesda, Md.) · 2025Review
- Predicting gene expression changes from chromatin structure modification.NPJ systems biology and applications · 2025Article
- Polymer models of chromatin organization in virally infected cells.Biochemical Society transactions · 2025Review
- Article
- Transcription processes compete with loop extrusion to homogenize promoter and enhancer dynamics.Science advances · 2024Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Chromatin folded into 3D macromolecular structures is often analyzed by chromosome conformation capture (3C) and fluorescence in situ hybridization (FISH) techniques, but these frequently provide contradictory results. Chromatin can be modeled as a simple polymer composed of a connected chain of units. By embedding data for epigenetic marks (H3K27ac), chromatin accessibility (assay for transposase-accessible chromatin using sequencing [ATAC-seq]), and structural anchors (CCCTC-binding factor [CTCF]), we developed a highly predictive heteromorphic polymer (HiP-HoP) model, where the chromatin fiber varied along its length; combined with diffusing protein bridges and loop extrusion, this model predicted the 3D organization of genomic loci at a population and single-cell level. The model was validated at several gene loci, including the complex Pax6 gene, and was able to determine locus conformations across cell types with varying levels of transcriptional activity and explain different mechanisms of enhancer use. Minimal a priori knowledge of epigenetic marks is sufficient to recapitulate complex genomic loci in 3D and enable predictions of chromatin folding paths.
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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.