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Related Experiment Video

Updated: Feb 22, 2026

The Power of Simplicity: Sea Urchin Embryos as in Vivo Developmental Models for Studying Complex Cell-to-cell Signaling Network Interactions
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Omics approaches to study gene regulatory networks for development in echinoderms.

Elijah K Lowe, Claudia Cuomo, Maria I Arnone

    Briefings in Functional Genomics
    |September 29, 2017
    PubMed
    Summary

    Emerging next-generation sequencing (NGS) approaches integrate multiple technologies to predict and validate gene interactions in echinoderm gene regulatory networks (GRNs). This enables genome-wide examination of developmental GRNs, especially in sea urchin embryos.

    Keywords:
    data integrationechinodermembryogene regulatory networksnext-generation sequencing

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    Area of Science:

    • Developmental Biology
    • Genomics
    • Systems Biology

    Background:

    • Gene regulatory networks (GRNs) are crucial for understanding developmental processes.
    • Traditional methods like perturbation experiments have been used to study GRNs, particularly in sea urchin embryos.
    • Next-generation sequencing (NGS) technologies offer advanced capabilities for genome and transcriptome analysis.

    Purpose of the Study:

    • To review emerging approaches integrating multiple NGS technologies for predicting and validating gene interactions in echinoderm GRNs.
    • To highlight the potential of these integrated approaches for reconstructing and experimentally testing developmental GRNs.
    • To discuss the application of these methods in both model and non-model organisms.

    Main Methods:

    • Integration of multiple NGS technologies (e.g., ATAC-seq, RNA-seq).
    • Application of computational approaches for prediction of gene interactions.
    • Experimental validation of predicted gene interactions through biological perturbations.
    • Comparative analysis across species with varying evolutionary distances.

    Main Results:

    • Emerging integrated NGS approaches facilitate the prediction and validation of gene interactions within echinoderm GRNs.
    • These methods enable genome-wide examination of GRNs, applicable to diverse species.
    • Echinoderms, particularly sea urchin embryos, are well-positioned for reconstructing and comparing developmental GRNs due to experimental accessibility and evolutionary diversity.

    Conclusions:

    • Advances in NGS and integrated omics approaches provide powerful tools for studying developmental GRNs on a genome-wide scale.
    • Experimental accessibility, including biological perturbation and cis-regulatory analyses, is key for successful GRN reconstruction.
    • Echinoderms offer a unique system for comparative studies of developmental GRNs due to their experimental tractability and evolutionary breadth.