Epigenomics and transcriptomics profiles of developing zebrafish heart cells

Chahal, G; Eichenlaub, MP; Tondl, M; Pawlak, M; Mohenska, M; Grimm, L; Bottrell, L; Drvodelic, M; Alaei, S; Hallab, J; Waylen, LN; Polo, JM; Blanpain, C; Palpant, N; Rossello, FJ; &#196;nk&#246;, ML; Currie, PD; Hogan, BM; Winata, C; Salimova, E; Nim, HT; Ramialison, M

Author(s): Chahal, G; Eichenlaub, MP; Tondl, M; Pawlak, M; Mohenska, M; Grimm, L; Bottrell, L; Drvodelic, M; Alaei, S; Hallab, J; Waylen, LN; Polo, JM; Blanpain, C; Palpant, N; Rossello, FJ; Änkö, ML; Currie, PD; Hogan, BM; Winata, C; Salimova, E; Nim, HT; Ramialison, M;
Details: Publication Year 2025-10-07,Volume 12,Issue #1,Page 1620
Journal Title: Scientific Data
Publication Type: Research article
Abstract: 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.
Publisher: Springer Nature
Keywords: Animals; *Zebrafish/genetics/embryology; *Transcriptome; *Myocytes, Cardiac; *Heart/embryology/growth & development; *Epigenomics; Gene Expression Profiling; Epigenesis, Genetic; Regulatory Sequences, Nucleic Acid; Gene Expression Regulation, Developmental
Department(s): Laboratory Research
Publisher's Version: https://doi.org/10.1038/s41597-025-05895-9
Open Access at Publisher's Site: https://doi.org/10.1038/s41597-025-05895-9
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2025-11-06 11:44:58

Last Modified: 2025-11-06 11:45:06