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Gastrulation

Gastrulation

Gastrulation establishes the three primary tissues of an embryo: the ectoderm, mesoderm, and endoderm. This developmental process relies on a series of intricate cellular movements, which in humans transforms a flat, “bilaminar disc” composed of two cell sheets into a three-tiered structure. In the resulting embryo, the endoderm serves as the bottom layer, and stacked directly above it is the intermediate mesoderm, and then the uppermost ectoderm. Respectively, these tissue strata...

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Author Spotlight: A Pipeline to Analyze Lineage-Specific Mutant Embryos at Single-Cell Resolution

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Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis.

Yinan Wan^1,2, Jakob El Kholtei^1,2, Ignatius Jenie³

¹Biozentrum, University of Basel, Basel, Switzerland.

Science (New York, N.Y.)

|March 12, 2026

Summary

Researchers developed a new whole-embryo imaging technique to map gene expression. This spatial transcriptomics approach reveals how gene activity drives embryonic development and cell differentiation.

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Area of Science:

Developmental Biology
Genomics
Molecular Biology

Background:

Gene expression patterns are crucial for embryonic development.
Systematic detection of gene expression in whole embryos has been a significant challenge.
Understanding spatiotemporal gene regulation is key to deciphering developmental processes.

Purpose of the Study:

To introduce a novel whole-embryo imaging platform for spatial transcriptomics.
To quantify gene expression patterns at subcellular resolution in zebrafish embryos.
To create a comprehensive online atlas of gene expression and chromatin accessibility during embryogenesis.

Main Methods:

Developed multiplexed error-robust fluorescent in situ hybridization (weMERFISH) for whole-embryo imaging.
Quantified expression of 495 genes in zebrafish embryos.
Integrated spatial transcriptomics data with live imaging and chromatin accessibility data.

Main Results:

Generated a detailed online atlas of 25,872 genes and 294,954 chromatin regions during embryogenesis.
Observed that gene expression patterns often reflect combinations of tissue-specific regulatory elements.
Demonstrated that developmental processes like morphogenesis and cell maturation correlate with gene expression changes.
Showed that sharp developmental boundaries arise from gene expression shifts, not solely cell sorting.
Revealed diverse dynamic mechanisms leading to similar expression patterns.

Conclusions:

Multiplexed whole-embryo spatial transcriptomics is now feasible.
This technology provides insights into the regulation and dynamics of embryonic gene expression.
The findings illuminate the interplay between gene regulation, chromatin accessibility, and developmental processes.