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The three-dimensional (3D) organization of chromosomes can be probed using methods like Capture-C. However, it is unclear how such population-level data relate to the organization within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modeling scheme based on the assumption that chromosome architecture is maintained by protein bridges, which form chromatin loops. To test the model, we perform FISH experiments and compare with Capture-C data. Starting merely from the locations of protein binding sites, our model accurately predicts the experimentally observed chromatin interactions, revealing a population of 3D conformations.

Original publication




Journal article


Genome Biol

Publication Date





Chromosome conformation, Fluorescence in situ hybridization, Polymer model, cis-regulation, Animals, Chromosomes, Mammalian, Computational Biology, Humans, In Situ Hybridization, Fluorescence, Mice, Models, Biological, Models, Molecular, Nucleic Acid Conformation, Polymers, Regulatory Sequences, Nucleic Acid