A developmental atlas for genes and cells.
The interplay between genes and cells during the development of a fertilized egg into an embryo is highly complex. Previous methods captured gene activity only in 2D slices, making whole-embryo visualization impossible and offering limited spatial detail, often missing subcellular patterns.
The new method now enables the research team to visualize the activities of thousands of genes throughout the entire embryo and link them to cell maturation and movement. The result is a comprehensive atlas of early development, along with new insights into how genes and cells shape the growing embryo. The study was published in Science.
The team developed a new imaging technology called weMERFISH. It enables the direct measurement of the activity of nearly 500 genes in entire tissues with subcellular resolution.
From these measurements, the researchers created an atlas of early embryonic development. “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,” says the author. The data are freely accessible through the web platform MERFISHEYES (http://schier.merfisheyes.com). “The atlas is intended as a resource for developmental biologists around the world.”
With the help of the atlas, the researchers were also able to clarify how clear boundaries between different tissues form, for example between muscle and backbone tissue. They discovered a zone of cells in which the activity of many genes changes dramatically and differs from one side to the other.
A comparison of early and later stages showed that these genes are initially active on both sides but later only on one. And there are hardly any cells that cross this boundary. “These boundaries do not arise because cells are intermingled and then sort, but mainly because cells change their genetic program,” says the author.
With weMERFISH, the MERFISHEYES atlas, and the integration of live imaging, researchers now have a new tool at their disposal. It allows the joint analysis of gene activity, gene regulation, and cell movement across the entire embryo. ScienceMission sciencenewshighlights https://sciencemission.com/atlas-for-genes-and-cells
Explore integrated single-cell RNA-seq, ATAC-seq, and MERFISH spatial imaging data from zebrafish embryonic development. Interactive 3D visualization from gastrulation to organogenesis.