{"doi":"10.1101/2023.09.14.557757","title":"Unique territorial and compartmental organization of chromosomes in the holocentric silkworm","abstract":"Abstract Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these are mainly observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is “secluded” from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. Polymer simulations show that this contact pattern can only be explained by high loop-extrusion activity within compartment S, combined with low extrusion elsewhere through the genome. This unique, targeted extrusion represents a novel phenomenon and underscores how evolutionarily conserved mechanisms—compartmentalization and loop extrusion—can be repurposed to create new 3D genome architectures.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":397296,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9401,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":900501,"name":"Emily Navarrete","orcid":"0000-0002-3986-8099","position":1,"is_corresponding":false},{"id":1173179,"name":"Clio Hockens","orcid":null,"position":2,"is_corresponding":false},{"id":490933,"name":"Nityananda Chowdhury","orcid":"0000-0002-8417-909X","position":3,"is_corresponding":false},{"id":1173180,"name":"Samuel R. Abraham","orcid":null,"position":4,"is_corresponding":false},{"id":1173181,"name":"Gaetan Cornilleau","orcid":null,"position":5,"is_corresponding":false},{"id":563360,"name":"Elissa P. Lei","orcid":"0000-0003-4894-0037","position":6,"is_corresponding":false},{"id":1022586,"name":"Julien Mozziconacci","orcid":"0000-0001-5652-0302","position":7,"is_corresponding":false},{"id":250608,"name":"Edward J. Banigan","orcid":"0000-0001-5478-7425","position":8,"is_corresponding":false},{"id":563359,"name":"Leah F. Rosin","orcid":"0000-0002-2489-4016","position":9,"is_corresponding":false},{"id":109520,"name":"Leonid A. Mirny","orcid":"0000-0002-0785-5410","position":10,"is_corresponding":false},{"id":1172895,"name":"Héloïse Muller","orcid":"0000-0003-0853-822X","position":11,"is_corresponding":false},{"id":539225,"name":"Ines A. Drinnenberg","orcid":"0000-0002-9649-0352","position":12,"is_corresponding":false},{"id":517940,"name":"Jesús Gil","orcid":"0000-0002-4303-6260","position":0,"is_corresponding":true}],"reference_count":109,"raw_metadata":null,"created_at":"2026-07-19T01:19:35.497854Z","pmid":"37745315","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":[]}