Polymer Physics Models Reveal Structural Folding Features of Single- Molecule Gene Chromatin Conformations

M Conte and A Abraham and A Esposito and LY Yang and JH Gibcus and KM Parsi and F Vercellone and A Fontana and F Di Pierno and J Dekker and M Nicodemi, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 25, 10215 (2024).

DOI: 10.3390/ijms251810215

Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2 Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments.

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