{"doi":"10.1534/g3.119.400402","title":"Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish Embryos","abstract":"<jats:title>Abstract</jats:title><jats:p>Epithelial cells are the building blocks of many organs, including skin. The vertebrate skin initially consists of two epithelial layers, the outer periderm and inner basal cell layers, which have distinct properties, functions, and fates. The embryonic periderm ultimately disappears during development, whereas basal cells proliferate to form the mature, stratified epidermis. Although much is known about mechanisms of homeostasis in mature skin, relatively little is known about the two cell types in pre-stratification skin. To define the similarities and distinctions between periderm and basal skin epithelial cells, we purified them from zebrafish at early development stages and deeply profiled their gene expression. These analyses identified groups of genes whose tissue enrichment changed at each stage, defining gene flow dynamics of maturing vertebrate epithelia. At each of 52 and 72 hr post-fertilization (hpf), more than 60% of genes enriched in skin cells were similarly expressed in both layers, indicating that they were common epithelial genes, but many others were enriched in one layer or the other. Both expected and novel genes were enriched in periderm and basal cell layers. Genes encoding extracellular matrix, junctional, cytoskeletal, and signaling proteins were prominent among those distinguishing the two epithelial cell types. In situ hybridization and BAC transgenes confirmed our expression data and provided new tools to study zebrafish skin. Collectively, these data provide a resource for studying common and distinguishing features of maturing epithelia.</jats:p>","journal":"G3 Genes|Genomes|Genetics","year":2019,"id":641694,"datarank":0.49983067652628066,"base_score":3.332204510175204,"endowment":3.332204510175204,"self_citation_contribution":0.49983067652628066,"citation_network_contribution":0.0,"self_endowment_contribution":0.49983067652628066,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":27,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"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":1668590,"name":"Maricruz De La Torre","orcid":null,"position":1,"is_corresponding":false},{"id":1668591,"name":"Eric F Medina","orcid":null,"position":2,"is_corresponding":false},{"id":747996,"name":"Jeffrey P. Rasmussen","orcid":"0000-0001-6997-3773","position":3,"is_corresponding":false},{"id":1668592,"name":"Joselyn Ramirez-Gutierrez","orcid":null,"position":4,"is_corresponding":false},{"id":355160,"name":"Alvaro Sagasti","orcid":"0000-0002-6823-0692","position":5,"is_corresponding":false},{"id":320811,"name":"Fang Wang","orcid":"0000-0001-8220-5226","position":6,"is_corresponding":false},{"id":1668589,"name":"Shawn J Cokus","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish Embryos","abstract":"<jats:title>Abstract</jats:title><jats:p>Epithelial cells are the building blocks of many organs, including skin. The vertebrate skin initially consists of two epithelial layers, the outer periderm and inner basal cell layers, which have distinct properties, functions, and fates. The embryonic periderm ultimately disappears during development, whereas basal cells proliferate to form the mature, stratified epidermis. Although much is known about mechanisms of homeostasis in mature skin, relatively little is known about the two cell types in pre-stratification skin. To define the similarities and distinctions between periderm and basal skin epithelial cells, we purified them from zebrafish at early development stages and deeply profiled their gene expression. These analyses identified groups of genes whose tissue enrichment changed at each stage, defining gene flow dynamics of maturing vertebrate epithelia. At each of 52 and 72 hr post-fertilization (hpf), more than 60% of genes enriched in skin cells were similarly expressed in both layers, indicating that they were common epithelial genes, but many others were enriched in one layer or the other. Both expected and novel genes were enriched in periderm and basal cell layers. Genes encoding extracellular matrix, junctional, cytoskeletal, and signaling proteins were prominent among those distinguishing the two epithelial cell types. In situ hybridization and BAC transgenes confirmed our expression data and provided new tools to study zebrafish skin. Collectively, these data provide a resource for studying common and distinguishing features of maturing epithelia.</jats:p>","is_dataset_classified":null,"base_score":3.332204510175204,"endowment":3.332204510175204,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"31431477","pmcid":"PMC6778804","openalex_id":"https://openalex.org/W2969535312","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"R25 GM062252","title":null},{"funder_name":"NEI NIH HHS","grant_id":"R21 EY024400","title":null},{"funder_name":"NIAMS NIH HHS","grant_id":"R01 AR064582","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM122901","title":null},{"funder_name":"National Science Foundation","grant_id":"1302873","title":"California State University Louis Stokes Alliance for Minority Participation (CSU-LSAMP) Senior Alliance (2013-2018)"},{"funder_name":"National Institutes of Health","grant_id":"3R25GM062252-02S1","title":"MBRS RISE at Cal State Dominguez"},{"funder_name":"National Institutes of Health","grant_id":"1R01GM122901-01","title":"Cytoskeletal control of microridge morphogenesis on mucosal epithelial cells of the zebrafish skin"},{"funder_name":"National Institutes of Health","grant_id":"5R21EY024400-02","title":"The morphogenesis of actin-based structures in mucosal epithelia"},{"funder_name":"National Institutes of Health","grant_id":"5R01AR064582-07","title":"Peripheral territory establishment by zebrafish somatosensory neurons"}],"total_grants":9,"fwci":1.2194,"citation_percentile":0.7569835,"influential_citations":0,"citation_trend":[{"year":2020,"count":4},{"year":2021,"count":3},{"year":2022,"count":5},{"year":2023,"count":2},{"year":2024,"count":4},{"year":2025,"count":6},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/g3journal/article-pdf/9/10/3439/37177058/g3journal3439.pdf","host_type":"journal"},{"url":"https://academic.oup.com/g3journal/article-pdf/9/10/3439/37177058/g3journal3439.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/g3journal/article-pdf/9/10/3439/37177058/g3journal3439.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1534/g3.119.400402","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/31431477","host_type":"repository"},{"url":"https://doaj.org/article/576cd58e4df1476eab8f646e3c46255d","host_type":"repository"},{"url":"https://escholarship.org/uc/item/5sx6n666","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6778804","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC6778804","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC6778804?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1534/g3.119.400402","host_type":""},{"url":"https://dx.doi.org/10.1534/g3.119.400402","host_type":""},{"url":"https://escholarship.org/content/qt5sx6n666/qt5sx6n666.pdf","host_type":""},{"url":"https://doi.org/https://doi.org/10.1534/g3.119.400402","host_type":""}],"fields_of_study":["Skin and Cellular Biology Research","Proteoglycans and glycosaminoglycans research","Wnt/β-catenin signaling in development and cancer","0301 basic medicine","03 medical and health sciences","0303 health sciences"],"mesh_terms":["Animals","Epithelium","Phenotype","Zebrafish","Gene Expression Regulation, Developmental","Gene Expression Profiling","Organogenesis","Embryonic Development","Transcriptome"],"keywords":["Biology","Zebrafish","Cell biology","Epidermis (zoology)","Transcriptome","Extracellular matrix","Gene","Cell type","In situ hybridization","Gene expression","Epithelium","Cell","Genetics","Anatomy","Epithelia","keratin","Skin Development","570","1.1 Normal biological development and functioning","Organogenesis","Embryonic Development","QH426-470","Investigations","576","Underpinning research","Animals","Developmental","Skin","Gene Expression Profiling","Statistics","Gene Expression Regulation, Developmental","Biological Sciences","Phenotype","Gene Expression Regulation","Biochemistry and cell biology","Biotechnology"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"},{"name":"doi"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-07T19:50:31.248757Z","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":[]}