{"doi":"10.1073/pnas.2108760119","title":"Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia","abstract":"Enhancers integrate transcription factor signaling pathways that drive cell fate specification in the developing brain. We paired enhancer labeling and single-cell RNA-sequencing (scRNA-seq) to delineate and distinguish specification of neuronal lineages in mouse medial, lateral, and caudal ganglionic eminences (MGE, LGE, and CGE) at embryonic day (E)11.5. We show that scRNA-seq clustering using transcription factors improves resolution of regional and developmental populations, and that enhancer activities identify specific and overlapping GE-derived neuronal populations. First, we mapped the activities of seven evolutionarily conserved brain enhancers at single-cell resolution in vivo, finding that the selected enhancers had diverse activities in specific progenitor and neuronal populations across the GEs. We then applied enhancer-based labeling, scRNA-seq, and analysis of in situ hybridization data to distinguish transcriptionally distinct and spatially defined subtypes of MGE-derived GABAergic and cholinergic projection neurons and interneurons. Our results map developmental origins and specification paths underlying neurogenesis in the embryonic basal ganglia and showcase the power of scRNA-seq combined with enhancer-based labeling to resolve the complex paths of neuronal specification underlying mouse brain development.","journal":"Proceedings of the National Academy of Sciences","year":2022,"id":248059,"datarank":0.519860385419959,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"self_citation_contribution":0.519860385419959,"citation_network_contribution":0.0,"self_endowment_contribution":0.519860385419959,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":31,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9512,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":367567,"name":"Anna Noren Rubin","orcid":"0000-0001-6190-2882","position":1,"is_corresponding":false},{"id":816098,"name":"Shanni N. Silberberg","orcid":"0000-0002-7979-9665","position":2,"is_corresponding":false},{"id":565709,"name":"Rinaldo Catta-Preta","orcid":"0000-0001-9833-1278","position":3,"is_corresponding":false},{"id":589432,"name":"Kenneth Lim","orcid":"0000-0002-0812-4513","position":4,"is_corresponding":false},{"id":565708,"name":"Athéna R. Ypsilanti","orcid":"0000-0002-0310-7693","position":5,"is_corresponding":false},{"id":567244,"name":"Iva Zdilar","orcid":"0000-0002-0080-3132","position":6,"is_corresponding":false},{"id":5490,"name":"Christopher S. McGinnis","orcid":"0000-0001-6923-9341","position":7,"is_corresponding":false},{"id":251029,"name":"Gabriel L. McKinsey","orcid":"0000-0002-5503-2830","position":8,"is_corresponding":false},{"id":816099,"name":"Thomas E. Rubino","orcid":"0000-0002-0139-3796","position":9,"is_corresponding":false},{"id":19890,"name":"Michael Hawrylycz","orcid":"0000-0002-5741-8024","position":10,"is_corresponding":false},{"id":59114,"name":"Carol L. Thompson","orcid":"0000-0003-1528-3237","position":11,"is_corresponding":false},{"id":5492,"name":"Zev J. Gartner","orcid":"0000-0001-7803-1219","position":12,"is_corresponding":false},{"id":435631,"name":"Luis Puelles","orcid":"0000-0002-9541-7073","position":13,"is_corresponding":false},{"id":23581,"name":"Hongkui Zeng","orcid":"0000-0002-0326-5878","position":14,"is_corresponding":false},{"id":247153,"name":"John L.R. Rubenstein","orcid":"0000-0002-4414-7667","position":15,"is_corresponding":false},{"id":6953,"name":"Alex S. Nord","orcid":"0000-0003-4259-7514","position":16,"is_corresponding":false},{"id":567243,"name":"Linda Su-Feher","orcid":"0000-0002-0660-7925","position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:24:09.893688Z","pmid":"35377797","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":[]}