Evidence map›Paper›PMID 41057362›Full record

ArticleScientific data2025

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 and 12 more

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Gulrez Chahal *Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Michael P Eichenlaub *Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Markus Tondl *Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Michał PawlakInstitute of Hematology and Blood Transfusion, Warsaw, Poland.
Monika MohenskaAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Lin GrimmDivision of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, QLD, Australia.
Lauren BottrellAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Mark DrvodelicAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Sara AlaeiAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Jeannette HallabAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Lisa N WaylenAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Jose M PoloAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Cédric BlanpainInterdisciplinary Research Institute (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, 1070, Belgium.
Nathan PalpantDivision of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, QLD, Australia.
Fernando J RosselloAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Minna-Liisa ÄnköAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Peter D CurrieAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Benjamin M HoganDivision of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, QLD, Australia.
Cecilia WinataInternational Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Ekaterina SalimovaAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia.
Hieu T NimAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia. hieu.nim@mcri.edu.au.
Mirana RamialisonAustralian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, Victoria, 3800, Australia. mirana.ramialison@mcri.edu.au.ORCID 0000-0001-6315-4777

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

EpigenomicsHeartMyocytes, CardiacTranscriptomeZebrafishAnimalsEpigenesis, GeneticGene Expression ProfilingGene Expression Regulation, DevelopmentalRegulatory Sequences, Nucleic Acid

Identifiers

PMID41057362
PMCPMC12504427

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.