ReviewChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology2017
Predicting chromatin architecture from models of polymer physics.
Review in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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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.
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Who cites it
25 citing papers in PubMed, 52 citations in OpenAlex.
- Article
- Endocrine therapy-specific lineage and partial epithelial-mesenchymal reprogramming defines divergent resistant cell-states in ER+ breast cancer.bioRxiv : the preprint server for biology · 2026Article
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
- 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
- Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome.Computational and structural biotechnology journal · 2024Article
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- Modification of surface characteristics of ophthalmic biomaterial-polymethyl methacrylate induced by cobalt 60 gamma irradiation.PloS one · 2023Article
- Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Cold Spring Harbor perspectives in biology · 2022Review
- Understanding 3D genome organization by multidisciplinary methods.Nature reviews. Molecular cell biology · 2021Review
- Review
- Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.Methods (San Diego, Calif.) · 2020Review
- Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies.Nature protocols · 2020Article
- Physical and data structure of 3D genome.Science advances · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Mapping the spectrum of 3D communities in human chromosome conformation capture data.Scientific reports · 2019Article
- Topological Constraints in Eukaryotic Genomes and How They Can Be Exploited to Improve Spatial Models of Chromosomes.Frontiers in molecular biosciences · 2019Article
- Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations.Nucleic acids research · 2018Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches. To identify the nature of architectural domains and their molecular determinants within a principled approach, we discuss models based on polymer physics. We show that basic concepts of interacting polymer physics explain chromatin spatial organization across chromosomal scales and cell types. The 3D structure of genomic loci can be derived with high accuracy and its molecular determinants identified by crossing information with epigenomic databases. In particular, we illustrate the case of the Sox9 locus, linked to human congenital disorders. The model in-silico predictions on the effects of genomic rearrangements are confirmed by available 5C data. That can help establishing new diagnostic tools for diseases linked to chromatin mis-folding, such as congenital disorders and cancer.
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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.