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<p><i>cis</i>-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 <i>cis</i>-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 <i>in vivo</i> 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 <i>popdc2</i> and <i>bmp10</i> 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>

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Epigenomics and transcriptomics profiles of developing zebrafish heart cells

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月7日

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  • 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

摘要

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.