{"doi":"10.1101/2022.02.17.480825","title":"Spatially resolved epigenomic profiling of single cells in complex tissues","abstract":"<jats:title>SUMMARY</jats:title>\n                <jats:p>The recent development of spatial omics methods enables single-cell profiling of the transcriptome and the 3D genome organization in a spatially resolved manner. Expanding the repertoire of spatial omics tools, a spatial epigenomics method will accelerate our understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved profiling of epigenomes in single cells using in-situ tagmentation and transcription followed by highly multiplexed imaging. We profiled histone modifications marking active promoters and enhancers, H3K4me3 and H3K27ac, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results further revealed putative promoter-enhancer pairs and enhancer hubs regulating the expression of developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.</jats:p>","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":null,"id":33694,"datarank":0.37216770394908266,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.08028118159078562,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.08028118159078562,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":6,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"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":175782,"name":"Cheen Euong Ang","orcid":null,"position":1,"is_corresponding":false},{"id":3627,"name":"Xiaowei Zhuang","orcid":"0000-0002-6034-7853","position":2,"is_corresponding":false},{"id":96239,"name":"Tian Lu","orcid":"0000-0002-1822-1229","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"36272405","pmcid":null,"openalex_id":"https://openalex.org/W4213082637","authors":[],"funders":[],"total_grants":0,"fwci":null,"citation_percentile":null,"influential_citations":4,"citation_trend":[{"year":2022,"count":3},{"year":2023,"count":1},{"year":2024,"count":2}],"oa_status":"green","license":"cc-by","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2022/02/19/2022.02.17.480825.full.pdf","host_type":"repository"},{"url":"https://www.cell.com/article/S0092867422012545/pdf","host_type":"GREEN"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2022/02/19/2022.02.17.480825.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2022.02.17.480825","host_type":"publisher"},{"url":"https://doi.org/10.1101/2022.02.17.480825","host_type":"repository"}],"fields_of_study":["Single-cell and spatial transcriptomics","Epigenetics and DNA Methylation","Genomics and Chromatin Dynamics","Medicine","Biology"],"mesh_terms":[],"keywords":["Epigenomics","H3K4me3","Epigenome","Enhancer","Biology","Computational biology","Epigenetics","Transcriptome","Tiling array","Histone","DNA methylation","Gene expression profiling","Profiling (computer programming)","Genetics","Promoter","Transcription factor","Gene","Gene expression","Computer science"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T16:42:59.787637Z","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":[]}