ArticleFrontiers in molecular biosciences2015
Current theoretical models fail to predict the topological complexity of the human genome.
Article in Frontiers in molecular biosciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps.bioRxiv : the preprint server for biology · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Review
- DNA-Topology Simplification by Topoisomerases.Molecules (Basel, Switzerland) · 2021Review
- Chromatin Is Frequently Unknotted at the Megabase Scale.Biophysical journal · 2020Article
- Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology.Science advances · 2020Article
- The Rabl configuration limits topological entanglement of chromosomes in budding yeast.Scientific reports · 2019Article
- Chromatin Loop Extrusion and Chromatin Unknotting.Polymers · 2018Article
- DNA knots occur in intracellular chromatin.Nucleic acids research · 2018Article
- Pathways of DNA unlinking: A story of stepwise simplification.Scientific reports · 2017Article
- A new model of sperm nuclear architecture following assessment of the organization of centromeres and telomeres in three-dimensions.Scientific reports · 2017Article
- Three-Color Chromosome Painting as Seen through the Eyes of mFISH: Another Look at Radiation-Induced Exchanges and Their Conversion to Whole-Genome Equivalency.Frontiers in oncology · 2016Article
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6 authors.
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Abstract
Understanding the folding of the human genome is a key challenge of modern structural biology. The emergence of chromatin conformation capture assays (e.g., Hi-C) has revolutionized chromosome biology and provided new insights into the three dimensional structure of the genome. The experimental data are highly complex and need to be analyzed with quantitative tools. It has been argued that the data obtained from Hi-C assays are consistent with a fractal organization of the genome. A key characteristic of the fractal globule is the lack of topological complexity (knotting or inter-linking). However, the absence of topological complexity contradicts results from polymer physics showing that the entanglement of long linear polymers in a confined volume increases rapidly with the length and with decreasing volume. In vivo and in vitro assays support this claim in some biological systems. We simulate knotted lattice polygons confined inside a sphere and demonstrate that their contact frequencies agree with the human Hi-C data. We conclude that the topological complexity of the human genome cannot be inferred from current Hi-C data.
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