Every cell in an animal’s body carries the same DNA. However, this single genetic blueprint somehow produces neurons that fire, muscles that contract, and tissues that perform completely different functions. How homologous genomes lead to this diversity remains one of the central mysteries of biology.
New research points to gene regulation — not genes alone — as the key to how diverse cell types emerge from a single genome. By analyzing ancient sea anemones cell by cell, researchers have built a detailed map linking DNA controls to how different cell types form. mentioned in Nature ecology and evolutionThe work suggests that the regulatory framework underlying the diversification of animal cells was already established early in evolutionary history.
“Expression tells us what cells do, but regulatory DNA tells us where they come from, how they develop, and from which germ layer they originate,” Dr. Marta Iglesias, co-first author of the study, said in an article. press release.
The roots of cellular diversity
Differences between cell types depend on how genes are controlled rather than on the genes themselves. However, most of what we understand about this process comes from a small number of well-studied species, leaving its deeper evolutionary origins unclear.
To explore those origins, the researchers turned to star sea anemones. Sea anemones, along with jellyfish and corals, belong to the cnidarians, one of the oldest animal groups to evolve, having first appeared about half a billion years ago. Despite their ancient lineage, cnidarians have specialized cell types, making them a valuable system for studying how cellular diversity first arose.
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Revealing cell identity in ancient sea anemones
To investigate how cell identity is built and maintained, the researchers analyzed nearly 60,000 individual cells from star sea anemones. Nematostella fitensis. The dataset included cells from two stages of life — adult animals and early gastrula embryos, when the basic body plan is still being established — allowing the team to capture both the developmental origins and mature states of the cells.
Rather than grouping the cells in which genes are active, the researchers focused on the regions of DNA that control gene activity. These regulatory elements act as control switches, determining when and where genes can be used. From this analysis, the team assembled a large catalog of more than 112,000 regulatory elements across the anemone genome – a surprisingly rich regulatory landscape for an animal of this size.
When cells were organized using these organizational patterns, a different picture emerged. Instead of grouping solely by function, cells are grouped according to their developmental origins, revealing the embryonic layers from which they arise. This made it possible to distinguish between cell types that perform similar roles but follow different developmental paths.
This distinction was particularly evident in muscle cells. Some muscle cells share similar functions and rely on many of the same genes, even though they originate from different embryonic layers. While the gene activity looked similar, the regulatory instructions controlling those genes were very different, showing that similar cell types can be built using different regulatory strategies.
Insights into the evolution of animal cell types
Cnidarians were among the first animals to develop specialized cell types such as neurons and muscle cells. They also developed a distinctive cell called a stinging cell, equipped with microscopic harpoon-like structures used for hunting and defence, which is the source of the familiar sting of jellyfish and sea anemones.
The results suggest that these early animals already had a flexible way to generate new cell types. By tracing how cell identities were built in an ancient animal, the study provides a new framework for understanding where animal cell types came from, and how today’s biological complexity emerged.
“This study opens up a whole new world of possibilities,” said co-author Arnau Sepe-Pedros. “From now on, we will investigate the evolution of animal cells by comparing genomic sequence information, and for the first time, we can do so systematically and on a large scale.”
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