{"doi":"10.1101/481598","title":"The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.</jats:p>","journal":null,"year":null,"id":614230,"datarank":0.5416376868966337,"base_score":3.6109179126442243,"endowment":3.6109179126442243,"self_citation_contribution":0.5416376868966337,"citation_network_contribution":0.0,"self_endowment_contribution":0.5416376868966337,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":36,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":2,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1582732,"name":"MEG Sauria","orcid":null,"position":1,"is_corresponding":false},{"id":562431,"name":"VE Hoskins","orcid":null,"position":2,"is_corresponding":false},{"id":1582733,"name":"X Wong","orcid":null,"position":3,"is_corresponding":false},{"id":1582734,"name":"E DeBoy","orcid":null,"position":4,"is_corresponding":false},{"id":1582735,"name":"M-C Gaillard","orcid":null,"position":5,"is_corresponding":false},{"id":1582736,"name":"P Tsang","orcid":null,"position":6,"is_corresponding":false},{"id":1582737,"name":"K Pekrun","orcid":null,"position":7,"is_corresponding":false},{"id":1582738,"name":"RA Ach","orcid":null,"position":8,"is_corresponding":false},{"id":1582739,"name":"NA Yamada","orcid":null,"position":9,"is_corresponding":false},{"id":116880,"name":"J Taylor","orcid":null,"position":10,"is_corresponding":false},{"id":561718,"name":"Karen Reddy","orcid":"0000-0003-4548-5999","position":11,"is_corresponding":false},{"id":1582731,"name":"TR Luperchio","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.</jats:p>","is_dataset_classified":null,"base_score":3.6109179126442243,"endowment":3.6109179126442243,"datacite_reuse_total":2,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"21097893","pmcid":null,"openalex_id":"https://openalex.org/W2903107497","authors":[],"funders":[{"funder_name":"National Institutes of Health","grant_id":"1U41HG006620-01","title":"Democratization of Data Analysis in Life Sciences Through Galaxy"},{"funder_name":"National Institutes of Health","grant_id":"5T32GM007445-33","title":"Biochemistry, Cellular and Molecular Biology Program"},{"funder_name":"National Institutes of Health","grant_id":"5R24DK106766-02","title":"VISION: ValIdated Systematic IntegratiON of epigenomic data"},{"funder_name":"National Institutes of Health","grant_id":"1R21AG050132-01A1","title":"Differential Protein Interactions in Hutchinson-Gilford Progeria Syndrome"}],"total_grants":4,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2019,"count":4},{"year":2020,"count":11},{"year":2021,"count":9},{"year":2022,"count":3},{"year":2023,"count":3},{"year":2024,"count":2},{"year":2025,"count":2},{"year":2026,"count":2}],"oa_status":"green","license":"cc-by-nc","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2018/11/29/481598.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2018/11/29/481598.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/481598","host_type":"publisher"},{"url":"https://doi.org/10.1101/481598","host_type":"repository"},{"url":"https://dx.doi.org/10.1101/481598","host_type":""},{"url":"http://dx.doi.org/10.1101/481598","host_type":""}],"fields_of_study":["Genomics and Chromatin Dynamics","RNA Research and Splicing","Chromosomal and Genetic Variations","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Nuclear lamina","Compartment (ship)","Lamin","Chromatin","Genome","Compartmentalization (fire protection)","Biology","Chromosome","Mitosis","Genomic organization","Cell biology","Gene","Genetics","Computational biology","Evolutionary biology","Nuclear protein","Transcription factor","Biochemistry"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.13211987.v1","title":"Additional file 1 of Inferring chromosome radial organization from Hi-C data","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.13211987","title":"Additional file 1 of Inferring chromosome radial organization from Hi-C data","publisher":"figshare","resource_type":"JournalArticle"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T11:46:30.625300Z","pmid":null,"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":[]}