Gulrez Chahal, Michael P Eichenlaub, Markus Tondl, Michał Pawlak, Monika Mohenska, Lin Grimm, Lauren Bottrell, Mark Drvodelic, Sara Alaei, Jeannette Hallab, Lisa N Waylen, Jose M Polo, Cédric Blanpain, Nathan Palpant, Fernando J Rossello, Minna-Liisa Änkö, Peter D Currie, Benjamin M Hogan, Cecilia Winata, Ekaterina Salimova, Hieu T Nim, Mirana Ramialison
{"title":"发育中的斑马鱼心脏细胞的表观基因组学和转录组学分析。","authors":"Gulrez Chahal, Michael P Eichenlaub, Markus Tondl, Michał Pawlak, Monika Mohenska, Lin Grimm, Lauren Bottrell, Mark Drvodelic, Sara Alaei, Jeannette Hallab, Lisa N Waylen, Jose M Polo, Cédric Blanpain, Nathan Palpant, Fernando J Rossello, Minna-Liisa Änkö, Peter D Currie, Benjamin M Hogan, Cecilia Winata, Ekaterina Salimova, Hieu T Nim, Mirana Ramialison","doi":"10.1038/s41597-025-05895-9","DOIUrl":null,"url":null,"abstract":"<p><p>cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocyte-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share several physiological features with the human heart during cardiogenesis. Here, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines in vivo transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform transgenic reporter assays for the identified cREs associated with popdc2 and bmp10 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cREs resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"1620"},"PeriodicalIF":6.9000,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12504427/pdf/","citationCount":"0","resultStr":"{\"title\":\"Epigenomics and transcriptomics profiles of developing zebrafish heart cells.\",\"authors\":\"Gulrez Chahal, Michael P Eichenlaub, Markus Tondl, Michał Pawlak, Monika Mohenska, Lin Grimm, Lauren Bottrell, Mark Drvodelic, Sara Alaei, Jeannette Hallab, Lisa N Waylen, Jose M Polo, Cédric Blanpain, Nathan Palpant, Fernando J Rossello, Minna-Liisa Änkö, Peter D Currie, Benjamin M Hogan, Cecilia Winata, Ekaterina Salimova, Hieu T Nim, Mirana Ramialison\",\"doi\":\"10.1038/s41597-025-05895-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocyte-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share several physiological features with the human heart during cardiogenesis. Here, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines in vivo transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform transgenic reporter assays for the identified cREs associated with popdc2 and bmp10 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cREs resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.</p>\",\"PeriodicalId\":21597,\"journal\":{\"name\":\"Scientific Data\",\"volume\":\"12 1\",\"pages\":\"1620\"},\"PeriodicalIF\":6.9000,\"publicationDate\":\"2025-10-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12504427/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Scientific Data\",\"FirstCategoryId\":\"103\",\"ListUrlMain\":\"https://doi.org/10.1038/s41597-025-05895-9\",\"RegionNum\":2,\"RegionCategory\":\"综合性期刊\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Scientific Data","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1038/s41597-025-05895-9","RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
Epigenomics and transcriptomics profiles of developing zebrafish heart cells.
cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocyte-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share several physiological features with the human heart during cardiogenesis. Here, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines in vivo transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform transgenic reporter assays for the identified cREs associated with popdc2 and bmp10 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cREs resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.
期刊介绍：
Scientific Data is an open-access journal focused on data, publishing descriptions of research datasets and articles on data sharing across natural sciences, medicine, engineering, and social sciences. Its goal is to enhance the sharing and reuse of scientific data, encourage broader data sharing, and acknowledge those who share their data.
The journal primarily publishes Data Descriptors, which offer detailed descriptions of research datasets, including data collection methods and technical analyses validating data quality. These descriptors aim to facilitate data reuse rather than testing hypotheses or presenting new interpretations, methods, or in-depth analyses.
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