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 of Prof. Alex Schier at the Biozentrum, University of Basel, 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.<\/p>\n
A 4D atlas for genes and cells<\/p>\n
\u201cA 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?\u201d says first author Yinan Wan. To answer this question, 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.<\/p>\n
From these measurements, the researchers created an atlas of early embryonic development. \u201cBy 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,\u201d says Wan. The data are freely accessible through the web platform MERFISHEYES (http:\/\/schier.merfisheyes.com). \u201cThe atlas is intended as a resource for developmental biologists around the world.\u201d<\/p>\n
When time becomes visible in space<\/p>\n
The images provide not just static snapshots but allow conclusions about spatial and temporal processes. For example, during tail formation, the researchers observed that cells along the body axis are arranged in a sequence of developmental stages: at the tip of the tail lie immature stem cells, while farther forward increasingly mature cells, such as muscle cells, can be found. \u201cIn a sense, you can see time in space,\u201d explains Wan. \u201cIt was also surprising that changes in gene activity align with how cells move through the embryo, linking gene expression dynamics to morphogenetic movements.\u201d\u00a0<\/p>\n
Sharp boundaries without cell sorting<\/p>\n
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. \u201cThese boundaries do not arise because cells are intermingled and then sort, but mainly because cells change their genetic program,\u201d says Alex Schier.<\/p>\n
Foundation for future studies<\/p>\n
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.
In the future, Schier\u2019s team plans to investigate additional developmental stages to further complete the picture of early vertebrate development. \u201cIn the long term, we want to understand which combinations of gene activity and cellular behavior are required to form a specific organ or tissue,\u201d says Schier. \u201cOne day we may find out how many ways there are to build a heart or a spinal cord.\u201d<\/p>\n
Reference: Wan Y, Kholtei JE, Jenie I, et al. Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis. Science. 2026;391(6790):eadt3439. doi: 10.1126\/science.adt3439<\/a><\/p>\n This article has been republished from the following materials<\/a>. Note: material may have been edited for length and content. For further information, please contact the cited source. Our press release publishing policy can be accessed here<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"The interplay between genes and cells during the development of a fertilized egg into an embryo is highly…\n","protected":false},"author":2,"featured_media":540006,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[49,48,66],"class_list":["post-540005","post","type-post","status-publish","format-standard","has-post-thumbnail","category-science","tag-ca","tag-canada","tag-science"],"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/posts\/540005","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/comments?post=540005"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/posts\/540005\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/media\/540006"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/media?parent=540005"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/categories?post=540005"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/ca\/wp-json\/wp\/v2\/tags?post=540005"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}