{"doi":"10.1101/2023.05.07.539762","title":"High-resolution spatial multi-omics reveals cell-type specific nuclear compartments","abstract":". Understanding nuclear organization requires identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci in individual cells, within complex tissues. Here, we introduce two-layer DNA seqFISH+, which allows simultaneous mapping of 100,049 genomic loci, together with nascent transcriptome for 17,856 genes and a diverse set of immunofluorescently labeled subnuclear structures all in single cells in cell lines and adult mouse cerebellum. Using these multi-omics datasets, we showed that repressive chromatin compartments are more variable by cell type than active compartments. We also discovered a single exception to this rule: an RNA polymerase II (RNAPII)-enriched compartment was associated with long, cell-type specific genes (> 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":389495,"datarank":1.1569656708737788,"base_score":3.4965075614664802,"endowment":3.4965075614664802,"self_citation_contribution":0.5244761342199721,"citation_network_contribution":0.6324895366538068,"self_endowment_contribution":0.5244761342199721,"citer_contribution":0.6324895366538068,"corpus_percentile":82.24646089579949,"corpus_rank":2296,"citation_count":32,"citer_count":32,"citers_with_citation_signal":27,"citers_with_endowment":27,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5803,"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":1159870,"name":"Yujing Yang","orcid":"0000-0002-1995-4029","position":1,"is_corresponding":false},{"id":340524,"name":"Jonathan A. White","orcid":"0000-0002-7009-3332","position":2,"is_corresponding":false},{"id":287804,"name":"Jina Yun","orcid":"0000-0002-7792-3749","position":3,"is_corresponding":false},{"id":90706,"name":"Meera Prasad","orcid":null,"position":4,"is_corresponding":false},{"id":1159871,"name":"Lincoln Ombelets","orcid":"0000-0002-5625-5411","position":5,"is_corresponding":false},{"id":816495,"name":"Simone Schindler","orcid":"0000-0003-1028-3115","position":6,"is_corresponding":false},{"id":552853,"name":"Long Cai","orcid":"0000-0002-7154-5361","position":7,"is_corresponding":false},{"id":616258,"name":"Yodai Takei","orcid":"0000-0002-7226-5185","position":0,"is_corresponding":true}],"reference_count":107,"raw_metadata":null,"created_at":"2026-07-19T01:18:27.054415Z","pmid":"37214923","pmcid":"PMC10197539","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":[]}