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Network architecture of transcriptomic stress responses in zebrafish embryos
Kaylee Beine1, Lauric Feugere2, Alexander P Turner3
1School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
Plos Computational Biology
|June 11, 2025
Summary
Zebrafish stress response genes are centrally located in protein-protein interaction networks. This network position correlates with gene expression and evolutionary conservation, offering insights into organismal responses to environmental stressors.
Area of Science:
- Genomics and Bioinformatics
- Ecology and Evolutionary Biology
- Developmental Biology
Background:
- Gene properties like expression and conservation relate to their position in protein-protein interaction (PPI) networks.
- Central genes are typically conserved and highly expressed, while peripheral genes are more adaptable.
- The stress response is hypothesized to be conserved and highly expressed, but empirical data is scarce.
Purpose of the Study:
- To investigate the relationship between the transcriptomic stress response and PPI network architecture in zebrafish embryos.
- To determine if environmental stressors (heat, UV) influence gene positioning within the PPI network.
- To explore how network position relates to gene expression changes and associated biological functions.
Main Methods:
- Analysis of zebrafish embryo transcriptomic data following exposure to heat and UV stress.
- Mapping differentially expressed genes onto the zebrafish protein-protein interaction network.
- Correlation analysis between gene network position, fold change, and Gene Ontology (GO) terms.
Main Results:
- Stress response genes are predominantly found in central positions within the PPI network.
- Heat stress genes occupied both central and peripheral network locations.
- UV stress genes were located in central to intermediate network positions.
- Network position correlated with the magnitude of gene expression changes and the diversity of associated GO terms.
- Differentially expressed genes across network positions affected shared phenotypes.
Conclusions:
- The zebrafish stress response exhibits conserved characteristics, as indicated by central network positioning of related genes.
- Specific environmental stressors (heat, UV) elicit distinct patterns in gene network localization.
- Understanding PPI network topology aids in deciphering the conserved and stressor-specific aspects of the organismal stress response.
- This approach can identify key regulators for understanding systemic responses to complex environmental changes in aquatic ecosystems.
