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.
Authors
- Monika Mohenska
- Mirana Ramialison (ORCID: https://orcid.org/0000-0001-6315-4777)
- Fernando J. Rossello (ORCID: https://orcid.org/0000-0003-3885-8777)
- Hieu T. Nim (ORCID: https://orcid.org/0000-0001-9320-0236)
- Markus Tondl (ORCID: https://orcid.org/0000-0002-6109-7438)
- Cecilia Lanny Winata
- Peter D. Currie (ORCID: https://orcid.org/0000-0001-8874-8862)
- Michał Pawlak (ORCID: https://orcid.org/0000-0001-7679-5493)
- Lin Grimm (ORCID: https://orcid.org/0000-0001-7807-2096)
- Michael Eichenlaub
- Gulrez Chahal (ORCID: https://orcid.org/0000-0002-7437-5417)
- Jeannette Hallab
- Ekaterina Salimova
- Sara Alaei (ORCID: https://orcid.org/0000-0003-4897-6339)
- Lisa N. Waylen (ORCID: https://orcid.org/0000-0002-9037-0886)
- Cédric Blanpain (ORCID: https://orcid.org/0000-0002-4028-4322)
- Benjamin M. Hogan (ORCID: https://orcid.org/0000-0002-0651-7065)
- Minna‐Liisa Änkö (ORCID: https://orcid.org/0000-0003-0446-3566)
- Nathan J. Palpant (ORCID: https://orcid.org/0000-0002-9334-8107)
- Mark Drvodelic
- J. M. Polo
- Lauren Bottrell
Institutions
- Université Libre de Bruxelles (BE)
- Royal Children's Hospital (AU)
- The University of Queensland (AU)
- Tampere University (FI)
- Peter MacCallum Cancer Centre (AU)
- Novo Nordisk Foundation (DK)
- Australian Regenerative Medicine Institute (AU)
- Hudson Institute of Medical Research (AU)
- Instytut Hematologii i Transfuzjologi (PL)
- International Institute of Molecular and Cell Biology (PL)
- South Australian Health and Medical Research Institute (AU)
- Murdoch Children's Research Institute (AU)
- The University of Adelaide (AU)
Publication Details
- Journal
- Scientific Data
- Published
- 2025-10-07
- DOI
- https://doi.org/10.1038/s41597-025-05895-9
- Primary Topic
- Congenital heart defects research
- Type
- article
- Field-Weighted Citation Impact
- 0.00