{"doi":"10.1101/2024.07.16.603769","title":"Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations","abstract":"Abstract Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2Mb 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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":491418,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8755,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":649992,"name":"Alex Abraham","orcid":"0000-0003-3533-6543","position":1,"is_corresponding":false},{"id":257691,"name":"Andrea Esposito","orcid":"0000-0002-5903-8439","position":2,"is_corresponding":false},{"id":109519,"name":"Liyan Yang","orcid":"0000-0002-3421-9866","position":3,"is_corresponding":false},{"id":109517,"name":"Johan H. Gibcus","orcid":"0000-0002-0851-7560","position":4,"is_corresponding":false},{"id":109518,"name":"Krishna Mohan Parsi","orcid":"0000-0002-6002-3816","position":5,"is_corresponding":false},{"id":1172587,"name":"Francesca Vercellone","orcid":"0000-0003-3933-8458","position":6,"is_corresponding":false},{"id":1172588,"name":"Andrea Fontana","orcid":"0009-0004-1996-4800","position":7,"is_corresponding":false},{"id":1269908,"name":"Florinda Di Pierno","orcid":null,"position":8,"is_corresponding":false},{"id":11679,"name":"Job Dekker","orcid":"0000-0001-5631-0698","position":9,"is_corresponding":false},{"id":257692,"name":"Mario Nicodemi","orcid":"0000-0002-8416-6416","position":10,"is_corresponding":false},{"id":257687,"name":"Mattia Conte","orcid":"0000-0002-6670-9800","position":0,"is_corresponding":true}],"reference_count":119,"raw_metadata":null,"created_at":"2026-07-19T02:08:45.247225Z","pmid":"39071404","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}