{"doi":"10.1242/dev.184432","title":"Enhancer transcription identifies <i>cis</i> -regulatory elements for photoreceptor cell types","abstract":"ABSTRACT Identification of cell type-specific cis-regulatory elements (CREs) is crucial for understanding development and disease, although identification of functional regulatory elements remains challenging. We hypothesized that context-specific CREs could be identified by context-specific non-coding RNA (ncRNA) profiling, based on the observation that active CREs produce ncRNAs. We applied ncRNA profiling to identify rod and cone photoreceptor CREs from wild-type and mutant mouse retinas, defined by presence or absence, respectively, of the rod-specific transcription factor (TF) Nrl. Nrl-dependent ncRNA expression strongly correlated with epigenetic profiles of rod and cone photoreceptors, identified thousands of candidate rod- and cone-specific CREs, and identified motifs for rod- and cone-specific TFs. Colocalization of NRL and the retinal TF CRX correlated with rod-specific ncRNA expression, whereas CRX alone favored cone-specific ncRNA expression, providing quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activity. We validated the activity of novel Nrl-dependent ncRNA-defined CREs in developing cones. This work supports differential ncRNA profiling as a platform for the identification of cell type-specific CREs and the discovery of molecular mechanisms underlying TF-dependent CRE activity.","journal":"Development","year":2020,"id":75861,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":22,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9571,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":395779,"name":"Linsin A. Smith","orcid":"0000-0003-2986-3232","position":1,"is_corresponding":false},{"id":296958,"name":"Rangarajan D. Nadadur","orcid":null,"position":2,"is_corresponding":false},{"id":395780,"name":"Andrew Hughes","orcid":"0000-0001-7788-3655","position":3,"is_corresponding":false},{"id":395781,"name":"Sui Wang","orcid":"0000-0003-1563-9117","position":4,"is_corresponding":false},{"id":395782,"name":"Joseph C. Corbo","orcid":"0000-0002-9323-7140","position":5,"is_corresponding":false},{"id":247143,"name":"Constance L. Cepko","orcid":"0000-0002-9945-6387","position":6,"is_corresponding":false},{"id":395783,"name":"Nicolas Lonfat","orcid":"0000-0001-7078-3301","position":7,"is_corresponding":false},{"id":270583,"name":"Ivan P. Moskowitz","orcid":"0000-0003-0014-4963","position":8,"is_corresponding":false},{"id":395778,"name":"Carlos Perez-Cervantes","orcid":"0000-0003-1352-7322","position":0,"is_corresponding":true}],"reference_count":103,"raw_metadata":null,"created_at":"2026-07-18T21:46:55.856612Z","pmid":"31915147","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":[]}