Beckwith K S, Ødegård-Fougner Ø, Morero N R, Barton C, Schueder F, Tang W, Alexander S, Peters J- M, Jungmann R, Birney E, Ellenberg J
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Dept. Biomedical Laboratory Science, Norwegian University of Science and Technology, Trondheim, Norway.
Nat Commun. 2025 Jul 19;16(1):6673. doi: 10.1038/s41467-025-61689-y.
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.
基因组的空间组织对其功能至关重要，包括基因表达和染色体分离。相分离和环状挤压被认为是构成区室和拓扑相关结构域的基础，然而，细胞核内基因组DNA的折叠是否与这些机制一致，很难在原位确定。在这里，我们提出了一种三维DNA追踪工作流程，可在单个结构保存良好的细胞中以纳米分辨率解析基因组结构。我们的研究结果表明，基因组DNA在100 kb尺度上通常表现为柔性无规卷曲。然而，在CTCF位点，我们在一部分细胞中发现了依赖黏连蛋白的环状结构，其构象在千碱基到兆碱基尺度上各不相同。我们在数百个单细胞中测量的三维折叠结构，使我们能够建立一个计算模型，解释单细胞中稀疏且动态的环状结构是如何构成在细胞群体中测量到的紧凑拓扑结构域的外观的。
