https://doi.org/10.1140/epjp/s13360-025-06026-4
Regular Article
Detecting higher-order chromosome interactions by polymer modeling
1
Dipartimento di Fisica, Università di Napoli Federico II, INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126, Naples, Italy
2
DIETI, Università di Napoli Federico II, Via Claudio 21, 80125, Naples, Italy
3
INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126, Naples, Italy
Received:
29
March
2024
Accepted:
13
January
2025
Published online:
28
January
2025
Recent experiments have revealed that human chromosomes have an intricate three-dimensional architecture in the cell nucleus, encompassing a hierarchy of interactions across multiple genomic scales. Despite those advances, detecting multiway DNA contacts at the single-molecule level remains challenging. Here, we use polymer physics models to investigate higher-order chromosomal contacts within a key genomic region in human colorectal cancer cells. By running extensive Molecular Dynamics simulations, we test model predictions against available experimental data and show that the model ensemble of single-molecule conformations significantly captures complex multiway chromosomal interactions beyond mere pairwise contacts.
© The Author(s) 2025
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