ArticleBiophysical journal2020
Chromatin Is Frequently Unknotted at the Megabase Scale.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 39 citations in OpenAlex.
- Conserved 3D genome reorganization during DNA repair.Life science alliance · 2026Review
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- Detection of Brain Cancer Using Genome-wide Cell-free DNA Fragmentomes.Cancer discovery · 2025Article
- Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis.Molecular cell · 2024Article
- DNA superhelicity.Nucleic acids research · 2024Article
- Geometric learning of knot topology.Soft matter · 2023Article
- Theory of chromatin organization maintained by active loop extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Homology of homologous knotted proteins.Journal of the Royal Society, Interface · 2023Article
- Topological gelation of reconnecting polymers.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Geometric Predictors of Knotted and Linked Arcs.ACS polymers Au · 2022Article
- Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions.Cold Spring Harbor perspectives in biology · 2022Review
- Modeling cell biological features of meiotic chromosome pairing to study interlock resolution.PLoS computational biology · 2022Article
- Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures.Polymers · 2021Article
- Article
- MGO on the go: Multiscale genome symposium - annual biophysical society meeting 2021.Biophysical reviews · 2021Article
- Parameter-free molecular super-structures quantification in single-molecule localization microscopy.The Journal of cell biology · 2021Article
- Multi-contact 3C reveals that the human genome during interphase is largely not entangled.Nature structural & molecular biology · 2020Article
- Article
- Multiscale Genome Organization: Dazzling Subject and Inventive Methods.Biophysical journal · 2020Article
- Active topological glass.Nature communications · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Knots in the human genome would greatly impact diverse cellular processes ranging from transcription to gene regulation. To date, it has not been possible to directly examine the genome in vivo for the presence of knots. Recently, methods for serial fluorescent in situ hybridization have made it possible to measure the three-dimensional position of dozens of consecutive genomic loci in vivo. However, the determination of whether genomic trajectories are knotted remains challenging because small errors in the localization of a single locus can transform an unknotted trajectory into a highly knotted trajectory and vice versa. Here, we use stochastic closure analysis to determine if a genomic trajectory is knotted in the setting of experimental noise. We analyze 4727 deposited genomic trajectories of a 2-Mb-long chromatin interval from human chromosome 21. For 243 of these trajectories, their knottedness could be reliably determined despite the possibility of localization errors. Strikingly, in each of these 243 cases, the trajectory was unknotted. We note a potential source of bias insofar as knotted contours may be more difficult to reliably resolve. Nevertheless, our data are consistent with a model in which, at the scales probed, the human genome is often free of knots.
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