A research team at the University of Basel announced on Mar. 12 a new imaging method that allows scientists to visualize the activity of thousands of genes throughout an entire zebrafish embryo. The technology, developed by Professor Alex Schier's group at the Biozentrum, provides a comprehensive atlas of all genes and cells involved in early embryonic development.
This advancement is significant because previous techniques could only capture gene activity in two-dimensional slices, limiting spatial detail and often missing important subcellular patterns. The new approach enables researchers to link gene activities with cell maturation and movement across the whole embryo, offering deeper insights into how complex organisms develop from a cluster of cells.
First author Dr. Yinan Wan said, "A central question has been: How do thousands of genes work together in an embryo, and how is their activity linked to the movement of cells?" To address this, the team created weMERFISH, a technology that directly measures nearly 500 genes' activity in entire tissues with subcellular resolution. Wan added, "By combining previous single-cell data with our gene activity measurements, we were able to calculate spatial patterns of thousands of genes and the activity of around 300,000 potential regulatory regions." The resulting data are available through the web platform MERFISHEYES (http://schier.merfisheyes.com). "The atlas is intended as a resource for developmental biologists around the world."
The images generated by this method allow researchers to observe not just static snapshots but also spatial and temporal processes during development. For example, during tail formation, immature stem cells are found at the tip while more mature muscle cells appear farther forward along the body axis. Wan explained, "In a sense, you can see time in space." She also noted that changes in gene activity align with how cells move through the embryo.
The atlas helped clarify how boundaries between different tissues form within embryos. Researchers discovered zones where many genes change their activity dramatically from one side to another. Comparing early and later stages showed these genes start active on both sides but later become restricted to one side; few cells cross these boundaries. Schier said, "These boundaries do not arise because cells are intermingled and then sort, but mainly because cells change their genetic program."
Looking ahead, Schier's team plans to use weMERFISH and MERFISHEYES to study additional developmental stages for a fuller picture of vertebrate development. Schier said, "In the long term, we want to understand which combinations of gene activity and cellular behavior are required to form a specific organ or tissue. One day we may find out how many ways there are to build a heart or a spinal cord."
