Epigenomics and transcriptomics profiles of developing zebrafish heart cells

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

Epigenomics and transcriptomics profiles of developing zebrafish heart cells

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

Biochemistry and Cell Biology

Research output: Contribution to journal › Article › Scientific › peer-review

1 Citation (Scopus)

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.

Original language	English
Journal	Scientific Data
DOIs	https://doi.org/10.1038/s41597-025-05895-9
Publication status	Published - 2025
MoE publication type	A1 Journal article-refereed

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Chahal, G., Eichenlaub, M. P., Tondl, M., Pawlak, M., Mohenska, M., Grimm, L., Bottrell, L., Drvodelic, M., Alaei, S., Hallab, J., Waylen, L. N., Polo, J. M., Blanpain, C., Palpant, N., Rossello, F. J., Änkö, M. L., Currie, P. D., Hogan, B. M., Winata, C., ... Ramialison, M. (2025). Epigenomics and transcriptomics profiles of developing zebrafish heart cells. Scientific Data. https://doi.org/10.1038/s41597-025-05895-9

@article{d3778e4cf780403cbe1345e6dde33a07,

title = "Epigenomics and transcriptomics profiles of developing zebrafish heart cells",

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.",

author = "Gulrez Chahal and Eichenlaub, \{Michael P.\} and Markus Tondl and Micha{\l} Pawlak and Monika Mohenska and Lin Grimm and Lauren Bottrell and Mark Drvodelic and Sara Alaei and Jeannette Hallab and Waylen, \{Lisa N.\} and Polo, \{Jose M.\} and C{\'e}dric Blanpain and Nathan Palpant and Rossello, \{Fernando J.\} and {\"A}nk{\"o}, \{Minna Liisa\} and Currie, \{Peter D.\} and Hogan, \{Benjamin M.\} and Cecilia Winata and Ekaterina Salimova and Nim, \{Hieu T.\} and Mirana Ramialison",

year = "2025",

doi = "10.1038/s41597-025-05895-9",

language = "English",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Nature Research",

}

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 2025, 'Epigenomics and transcriptomics profiles of developing zebrafish heart cells', Scientific Data. https://doi.org/10.1038/s41597-025-05895-9

TY - JOUR

T1 - Epigenomics and transcriptomics profiles of developing zebrafish heart cells

AU - Chahal, Gulrez

AU - Eichenlaub, Michael P.

AU - Tondl, Markus

AU - Pawlak, Michał

AU - Mohenska, Monika

AU - Grimm, Lin

AU - Bottrell, Lauren

AU - Drvodelic, Mark

AU - Alaei, Sara

AU - Hallab, Jeannette

AU - Waylen, Lisa N.

AU - Polo, Jose M.

AU - Blanpain, Cédric

AU - Palpant, Nathan

AU - Rossello, Fernando J.

AU - Änkö, Minna Liisa

AU - Currie, Peter D.

AU - Hogan, Benjamin M.

AU - Winata, Cecilia

AU - Salimova, Ekaterina

AU - Nim, Hieu T.

AU - Ramialison, Mirana

PY - 2025

Y1 - 2025

N2 - 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.

AB - 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.

UR - https://researchportal.tuni.fi/en/publications/113fbe39-52d6-4600-a2b9-e254af5754ab

U2 - 10.1038/s41597-025-05895-9

DO - 10.1038/s41597-025-05895-9

M3 - Article

C2 - 41057362

SN - 2052-4463

JO - Scientific Data

JF - Scientific Data

ER -

Epigenomics and transcriptomics profiles of developing zebrafish heart cells

Abstract

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