{"doi":"10.1016/j.celrep.2023.113543","title":"Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids","abstract":"We have generated a high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive stage-specific alterations in DNA topology and correlate these changes with transcription of cell-type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift toward A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression, respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages (i.e., TAD cliques) localize in active chromatin regions with binding sites for eye-field transcription factors. These genes gain chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.","journal":"Cell Reports","year":2023,"id":352066,"datarank":0.3453877639491069,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.0,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9276,"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":301400,"name":"Zachary Batz","orcid":"0000-0002-4483-2402","position":1,"is_corresponding":false},{"id":565088,"name":"Nivedita Singh","orcid":"0000-0001-5919-1161","position":2,"is_corresponding":false},{"id":554744,"name":"Claire Marchal","orcid":"0000-0001-8253-2665","position":3,"is_corresponding":false},{"id":54657,"name":"Anand Swaroop","orcid":"0000-0002-1975-1141","position":4,"is_corresponding":false},{"id":632674,"name":"Zepeng Qu","orcid":"0000-0003-1208-0557","position":0,"is_corresponding":true}],"reference_count":147,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:12:50.107998Z","pmid":"38048222","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":[]}