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Related Experiment Video

Updated: Jan 14, 2026

Large-scale Zebrafish Embryonic Heart Dissection for Transcriptional Analysis
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Elucidating cardiomyocyte state transitions in zebrafish heart development using transcriptome dynamics.

Dongxu Jin1, Yihao Zhu1, Yao Zu2

  • 1International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.

Biochemical and Biophysical Research Communications
|October 19, 2025
PubMed
Summary

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This study used zebrafish to map gene expression during heart development, identifying key genes like smtnl1 involved in congenital heart disease (CHD). Understanding these genetic drivers is crucial for CHD research.

Area of Science:

  • Developmental Biology
  • Genetics
  • Cardiovascular Research

Background:

  • Congenital heart disease (CHD) is the most common birth defect, but its genetic underpinnings are not fully understood.
  • Investigating the molecular mechanisms of heart development is essential for identifying causes of CHD.

Purpose of the Study:

  • To investigate transcriptional dynamics during cardiac morphogenesis using a zebrafish model.
  • To identify key genes and molecular pathways involved in heart development and CHD pathogenesis.

Main Methods:

  • Utilized zebrafish embryos for cardiac morphogenesis studies.
  • Performed Bulk RNA sequencing (Bulk RNA-seq) and single-cell RNA sequencing (scRNA-seq) at multiple embryonic stages (24-48 hpf).
  • Employed weighted gene co-expression network analysis and pseudotime analysis.
Keywords:
Heart developmentSingle-cell transcriptomicsTime seriesTranscriptomicsZebrafish

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Main Results:

  • Linked gene expression dynamics to specific cardiac morphogenetic events (heart tube formation, chamber formation, looping, valve formation).
  • Identified a critical gene module (M5) associated with cardiomyocyte state transitions during development.
  • Discovered smoothelin like 1 (smtnl1) as a hub gene; its knockout led to cardiac dysfunction in zebrafish.

Conclusions:

  • Delineated stage-specific molecular drivers of embryonic heart development.
  • Identified candidate genes, including smtnl1, for further investigation into CHD pathogenesis.
  • Highlighted the utility of zebrafish models for studying complex congenital anomalies.