ArticleBiophysical journal2021
Three-dimensional loop extrusion.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 0 citations in OpenAlex.
- The physical chemistry of interphase loop extrusion.Cell genomics · 2026Article
- Yeast condensin acts as a transient intermolecular crosslinker in entangled DNA.Nucleic acids research · 2026Article
- Motorized chromosome models of mitotic chromosome folding.Nature communications · 2025Article
- Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search.Nucleic acids research · 2025Article
- Barrier effects on the kinetics of cohesin-mediated loop extrusion.Biophysical journal · 2025Article
- Motor domain of condensin and step formation in extruding loop of DNA.Journal of biological physics · 2024Article
- Anisotropic scrunching of SMC with a baton-pass mechanism.Communications biology · 2024Review
- Replicating Chromosomes in Whole-Cell Models of Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.PLoS computational biology · 2023Article
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
- DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations.Nucleic acids research · 2022Article
- Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Loop extrusion convincingly describes how certain structural maintenance of chromosome (SMC) proteins mediate the formation of large DNA loops. Yet most of the existing computational models cannot reconcile recent in vitro observations showing that condensins can traverse each other, bypass large roadblocks, and perform steps longer than their own size. To fill this gap, we propose a three-dimensional (3D) "trans-grabbing" model for loop extrusion, which not only reproduces the experimental features of loop extrusion by one SMC complex but also predicts the formation of so-called Z-loops via the interaction of two or more SMCs extruding along the same DNA substrate. By performing molecular dynamics simulations of this model, we discover that the experimentally observed asymmetry in the different types of Z-loops is a natural consequence of the DNA tethering in vitro. Intriguingly, our model predicts this bias to disappear in the absence of tethering and a third type of Z-loop, which has not yet been identified in experiments, to appear. Our model naturally explains roadblock bypassing and the appearance of steps larger than the SMC size as a consequence of non-contiguous DNA grabbing. Finally, this study is the first, to our knowledge, to address how Z-loops and bypassing might occur in a way that is broadly consistent with existing cis-only 1D loop extrusion models.
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