Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ
The spatial organization of the genome is essential for its functions, including gene expression and chromosome segregation. Phase separation and loop extrusion have been proposed to underlie compartments and topologically associating domains, however, whether the fold of genomic DNA inside the nucleus is consistent with such mechanisms has been difficult to establish in situ. Here, we present a 3D DNA-tracing workflow that resolves genome architecture in single structurally well-preserved cells with nanometre resolution. Our findings reveal that genomic DNA generally behaves as a flexible random coil at the 100-kb scale. At CTCF sites however, we find Cohesin-dependent loops in a subset of cells, in variable conformations from the kilobase to megabase scale. The 3D-folds we measured in hundreds of single cells allowed us to formulate a computational model that explains how sparse and dynamic loops in single cells underlie the appearance of compact topological domains measured in cell populations.
Authors
- Florian Schueder (ORCID: https://orcid.org/0000-0003-3412-5066)
- Carl Barton (ORCID: https://orcid.org/0000-0001-6938-9446)
- Jan Ellenberg (ORCID: https://orcid.org/0000-0001-5909-701X)
- Ralf Jungmann (ORCID: https://orcid.org/0000-0003-4607-3312)
- Stephanie Alexander (ORCID: https://orcid.org/0000-0002-8308-3977)
- Jan‐Michael Peters (ORCID: https://orcid.org/0000-0003-2820-3195)
- Kai Sandvold Beckwith (ORCID: https://orcid.org/0000-0001-5598-5482)
- Ewan Birney (ORCID: https://orcid.org/0000-0001-8314-8497)
- Weixin Tang (ORCID: https://orcid.org/0000-0002-5739-5416)
- Natalia Rosalía Morero (ORCID: https://orcid.org/0000-0003-0092-5663)
Institutions
- European Bioinformatics Institute (GB)
- Research Institute of Molecular Pathology (AT)
- Norwegian University of Science and Technology (NO)
- Norwegian Cancer Society (NO)
- Center for NanoScience (DE)
- ETH Zurich (CH)
- European Molecular Biology Laboratory (DE)
- Vienna Biocenter (AT)
- Max Planck Institute of Biochemistry (DE)
- European Molecular Biology Laboratory (DE)
- Ludwig-Maximilians-Universität München (DE)
- KTH Royal Institute of Technology (SE)
- Birkbeck, University of London (GB)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-07-19
- DOI
- https://doi.org/10.1038/s41467-025-61689-y
- Citations
- 8
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 6.45
Funders
- Alexander von Humboldt-Stiftung
- European Molecular Biology Laboratory
- European Commission
- Vienna Science and Technology Fund
- Österreichische Forschungsförderungsgesellschaft
- National Institutes of Health
- Common Fund