ArticleNucleic acids research2023
Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A scaffolding element rewires local 3D chromatin architecture during differentiation.Nature communications · 2026Article
- Genome-wide absolute quantification of chromatin looping.Nature structural & molecular biology · 2026Article
- Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells.bioRxiv : the preprint server for biology · 2026Article
- TAD boundaries and gene activity are uncoupled.eLife · 2026Article
- TAD boundaries and gene activity are uncoupled.bioRxiv : the preprint server for biology · 2026Article
- Uniform dynamics of cohesin-mediated loop extrusion in living human cells.Nature genetics · 2025Article
- DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes.Histochemistry and cell biology · 2024Article
- Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.Nucleic acids research · 2023Article
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4 authors.
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Abstract
Genome-wide chromosome conformation capture (Hi-C) has revealed the organization of chromatin into topologically associating domains (TADs) and loops, which are thought to help regulate genome functions. TADs and loops are understood as the result of DNA extrusion mediated by the cohesin complex. However, despite recent efforts, direct visualization and quantification of this process in single cells remains an open challenge. Here, we use polymer simulations and dedicated analysis methods to explore if, and under which conditions, DNA loop extrusion can be detected and quantitatively characterized by imaging pairs of fluorescently labeled loci located near loop or TAD anchors in fixed or living cells. We find that under realistic conditions, extrusion can be detected and the frequency of loop formation can be quantified from fixed cell images alone, while the lifetime of loops and the speed of extrusion can be estimated from dynamic live-cell data. Our delineation of appropriate imaging conditions and the proposed analytical methods lay the groundwork for a systematic quantitative characterization of loop extrusion in fixed or living cells.
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