---
title: A Transparent Fish Keeps Using Limb-Building Genes in Its Adult Fins
description: Whitehead scientists profiled 600,000+ cells of the transparent fish Danionella cerebrum in what they call the first whole-body atlas of an adult vertebrate.
author: Darie Nani (Editor-in-Chief)
date: 2026-10-30T12:05:32.307Z
updated: 2026-10-30T12:05:32.328Z
canonical: https://www.sovereignmagazine.com/article/danionella-whole-body-cell-atlas-adult-vertebrate
image: https://cdn.nanimediahouse.com/danionella-cerebrum-transparent-fish-511113.webp
categories: Science & Tech
content_type: News
region: Global
publication: Sovereign Magazine
schema_type: Article
---

Cells in the fins of an adult Danionella cerebrum, a transparent fish about 12 millimeters long, are still running gene programs that other vertebrates use to form forelimbs and hindlimbs. Scientists at the Whitehead Institute made that finding while recording which genes are active in cells from across the fish's whole body. They also watched the fish regrow neurons lost from an injured forebrain.

The team, led by postdoctoral researcher Kutay Deniz Atabay in the lab of Peter Reddien, published the work in Science on October 29 and describes it as the first comprehensive whole-body single-cell atlas of an adult vertebrate. Each entry in the atlas is a cell's transcriptome, the full set of RNA molecules the cell has made from its DNA at a given time, which shows which genes it is using. From more than 600,000 such snapshots, researchers can look up the fish's cell types, the genes that set each type apart and, for many of them, where in the body they sit.

## Adult Cells Keep Gene Activity Tied to Their Place in the Body

Fibroblasts, the cells of connective tissue, kept up region-specific activity in genes best known for laying out body parts during development. The limb programs in the pectoral and pelvic fins are one example. What those signals do in an adult fish is unknown. The researchers suggest they may help tissues maintain or rebuild the right structures, as positional information does in planarians, flatworms that regrow lost tissue and that Reddien's lab had already mapped as whole animals.

## Neurons Group by Brain Region More Than by Neurotransmitter

In the nervous system, neurons tended to group by brain region rather than by the neurotransmitter they use to signal. Neurons from the same region often had more similar gene activity than neurons using the same chemical in different regions, a pattern also seen in other vertebrates, including mammals. The researchers take it as a sign that a neuron's region and developmental origin may be an important organizing feature of vertebrate nervous systems.

## The Fish Regrew Neurons Lost From an Injured Forebrain

When the researchers injured the telencephalon, a region of the forebrain, the lost neurons grew back. They traced the repair from an early wound and immune response to activity in neural stem cells, and then to the production and maturation of new neurons.

Adult humans make only a meager number of new neurons, mostly in the hippocampus, the brain's memory center, according to Columbia University Irving Medical Center, whose scientists study brain repair in zebrafish. Danionella is a close relative of zebrafish, so zebrafish genetic tools work on it. It now also has a reference map of its healthy cells, against which repair, injury, aging or the effects of drugs can be measured cell by cell across the whole body.

## Most Vertebrates Are Too Large to Profile Cell by Cell

The authors wrote in the paper that mapping cell transcriptomes across an entire adult vertebrate "has not been achieved, largely because most vertebrates are too large for comprehensive molecular access to their cellular and molecular complexity." Profiling every tissue of a larger animal is technically demanding and expensive. The adult fruit fly, an invertebrate, was mapped across its whole body in 2022.

Atabay became interested in Danionella in early 2019, while looking for a small, transparent animal in which he could watch a nervous system regenerate. The species was adopted for neuroscience research in 2018 and formally described in 2021, and its brain is visible through the top of its head. "Deniz and I had the thought: Would it be possible to get a cell-type transcriptome atlas for a complete vertebrate?" said Reddien, who is also a professor of biology at MIT and a Howard Hughes Medical Institute Investigator. "Here's an animal where we'd have a chance."

## The Team Sequenced Cells From Every Tissue and Mapped Them Back in Place

The team ran single-cell RNA sequencing on cells from the brain, spinal cord, eyes, internal organs, fins, head and trunk, then used spatial methods to place each cell type and its gene activity back in the tissue it came from, picking up even exceptionally rare cell populations. "Once you have a spatially resolved atlas, you know what cell types exist, but you also know the neighbors of those cell types in this context," Atabay said.

The atlas is public through [DigiFish](https://digifish.wi.mit.edu/atlas/tissue/atlas), an interactive resource. Because the fish is transparent, researchers can use it to choose cells and genes to study or manipulate, then follow their activity in the living animal.

More on the study is at [the Whitehead Institute](https://wi.mit.edu/news/researchers-create-first-whole-body-single-cell-atlas-adult-vertebrate).

## FAQ

**Q: How big is Danionella cerebrum?**
It is one of the smallest vertebrates in the world. The authors wrote that it has the smallest vertebrate brain on record: about 650,000 neurons in 0.6 cubic millimeters, roughly four times the size of a fruit fly's brain but with all the major vertebrate brain regions. Its genome is about half the size of the zebrafish genome.

**Q: How did the team see where each cell sits in the body?**
They used two spatial techniques, MERFISH and HCR-FISH. Both are fluorescent in situ hybridization methods, which make RNA molecules glow in place inside intact tissue, so a cell type found by sequencing can be located on the animal.

**Q: Does the adult fish keep juvenile traits?**
Yes. In a preprint of the study, the authors said the atlas "uncovered paedomorphic features," meaning adult traits that resemble juvenile ones.