Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations
Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2 Mb wide genomic region encompassing the human <i>LTN1</i> gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in silico the ensemble of single-molecule <i>LTN1</i> 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.
Authors
- Krishna Mohan Parsi (ORCID: https://orcid.org/0000-0002-6002-3816)
- Liyan Yang (ORCID: https://orcid.org/0000-0002-3421-9866)
- Job Dekker (ORCID: https://orcid.org/0000-0001-5631-0698)
- Mario Nicodemi (ORCID: https://orcid.org/0000-0002-8416-6416)
- Mattia Conte (ORCID: https://orcid.org/0000-0002-6670-9800)
- Alex Abraham (ORCID: https://orcid.org/0000-0003-3533-6543)
- Francesca Vercellone (ORCID: https://orcid.org/0000-0003-3933-8458)
- Johan H. Gibcus (ORCID: https://orcid.org/0000-0002-0851-7560)
- Andrea Esposito (ORCID: https://orcid.org/0000-0002-5903-8439)
- Andrea Fontana (ORCID: https://orcid.org/0009-0004-1996-4800)
- Florinda Di Pierno
Institutions
- Howard Hughes Medical Institute (US)
- University of Massachusetts Chan Medical School (US)
- Ingegneria dei Trasporti (Italy) (IT)
- Istituto Nazionale di Fisica Nucleare, Sezione di Napoli (IT)
Publication Details
- Journal
- International Journal of Molecular Sciences
- Published
- 2024-09-23
- DOI
- https://doi.org/10.3390/ijms251810215
- Citations
- 3
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 0.70
Funders
- Università degli Studi di Napoli Federico II