Biology subjects

Tanaka, E. M.

Publications and source records attributed to Tanaka, E. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Minimal essential requirements for neural tube self-organisation

The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from pluripotent stem cells (PSCs) provide powerful systems for identifying principles governing tissue self-organisation. Neural tube organoids (NTOs), initiated from single PSCs with a pulse of retinoic acid (RA), self-organise into structures containing floorplate cells that secrete SHH morphogen to pattern adjacent neural tissue. Yet, how the initial cellular diversity arises and how appropriate cell-type proportions are allocated has remained unclear. Here, using time-resolved single-cell transcriptomics, quantitative immunofluorescence, and dynamical systems modelling we show that RA triggers a transient co-expression state of the transcription factors PAX6 and FOXA2 from which cells asynchronously resolve into two opposing fates: PAX6 neural precursors and FOXA2 floorplate precursors. PAX6 and FOXA2 are both necessary and sufficient to reconstitute self-organisation, establishing these transcription factors as key determinants of emergent tissue pattern. Rather than operating as a simple feed-forward system in which cells are guided solely by RA, feedback between the alternative cell fates, mediated by BMP signalling from floorplate precursors, determines cell type proportions and ensures reproducible cell-type diversity in each NTO. This dual expression state was also identified in mouse embryos, demonstrating how in vitro models inform in vivo biology. These findings establish a general design strategy - symmetry breaking through opposing fate determinants coupled to proportioning via signal feedback control - that may operate broadly across developmental contexts to generate tissues with predictable cellular compositions.

developmental biology↗

bioRxiv2026

Axolotl tail regeneration emerges during a defined embryonic window

How regenerative capacity originates during development remains poorly understood, even in vertebrates with exceptional adult regenerative ability. Using the axolotl, we identify a defined embryonic window between stages 30 and 34 during which the tail region transitions from a regeneration-incompetent to a regeneration-competent state. Amputations across staged embryos reveal that earlier embryos entirely fail to regenerate, whereas later embryos regenerate functional tails. Notably, tail stumps from nonregenerating embryos can recover the ability to regenerate when reamputated at later stages, demonstrating that early regenerative failure does not permanently impair regenerative capacity. This differs from the transient refractory period described in Xenopus, where regenerative competence is lost and reacquired around the end of tail outgrowth, and indicates that staged acquisition of regenerative competence is a broadly shared but mechanistically distinct feature of amphibian development. To determine whether this transition reflects changes in progenitor composition, we analysed the single-cell transcriptional landscapes of axolotl tail buds across this window. Tail bud progenitors, including neuromesodermal progenitors, persist through the transition, indicating that the onset of regenerative competence is unlikely to be explained by the loss of embryonic progenitors. Finally, using Tbxt (Brachyury) crispant axolotls with severe axial defects, we show that tail regeneration occurs effectively despite earlier abnormal embryonic tail development, with functional uncoupling of the mechanisms of tail development and regeneration. This framework provides new opportunities for identifying the drivers of regenerative competence and understand why this capacity is lost in other vertebrate species.

developmental biology↗

bioRxiv2026

Adult regenerative defects arise from discordant scaling of signal dependent growth and patterning

Orders of magnitude distinguish an organs size in adulthood from its size when patterning was established during embryonic development. The prospect of engineering adult organ regeneration raises the fundamental question of whether regenerative stem cell patterning should be elicited at embryonic or adult scale. Axolotls regenerate their limbs at all stages of post-embryonic life, encompassing an order of magnitude increase in animal size, but the mechanisms allowing this robust capacity remain unclear. Limb regeneration occurs by the formation of an embryonic-like progenitor zone, the blastema, whose dimensions increase with animal size, suggesting that at least some aspects of limb regeneration must scale. Here, by combining spatial transcriptomics, biophysical modelling, quantitative imaging, and functional perturbations, we found distinct scaling signatures among key signaling pathways, arguing against a body-size-dependent hormonal scaling mechanism. SHH signaling showed partial scaling that saturated in largest adult sizes, with a correspondingly early termination of blastema growth while Wnt9a-modulated digit patterning scaled at all animal sizes. As a result of this differential scaling, digit patterning wavelength was mismatched with respect to domain growth in the largest blastemas, preventing the addition of the last digit. In agreement with this model, regenerative failure can be rescued by timed supplementation of SHH. Our results show that coordinated scaling of morphogen signaling is a key requirement for adult organ regeneration.

systems biology↗

bioRxiv2026

Recursive Repeat Extender (RRE): A recursive approach to automatically extend repeat element models

Repetitive elements, including transposable elements (TEs), are integral structural components of eukaryotic genomes; consequently, their identification and classification are crucial to their study. Several approaches have been developed to perform de novo genome-wide repeat identification through pairwise sequence comparisons; however, they often generate truncated repeat models due to their sampling strategies and the substantial fragmentation of many of the older repeat copies in the genome. To improve repeat models generated de novo, several algorithms have been developed that increase model length via the BEEA (BLAST-Extend-Extract-Align) approach, in which genomic instances of each repeat are identified with BLAST, their coordinates are extended, and a refined model is generated by aligning the extended sequences. Nevertheless, these extension algorithms exhibit two key limitations that hinder the reconstruction of highly degenerate and fragmented repeats: the use of BLAST as a search algorithm - which limits their sensitivity in detecting highly diverged sequences - and the use of a single search step, which precludes the reconstruction of extensively fragmented repeat models. In this work, we present a novel approach to extend repeat models, called RRE (Recursive Repeat Extender), which uses profile hidden Markov models (HMMs) to search for repeat elements with high sensitivity and employs a recursive extension strategy that iteratively searches and extends the repeat model, using the extended model from each round as input for the next and continuing until no additional sequence can be incorporated. We apply RRE to repeat libraries generated de novo from five model organisms, and our results show that RRE-generated repeat libraries contain fewer but longer repeat models and can identify a larger proportion of the genomes as repetitive than RepeatModeler2-generated repeat libraries. Notably, RRE can reconstruct highly degenerate repeats such as CR1_Mam, producing a model that achieves similar coverage to the reference Dfam model while extending it by an additional 131 bp that were not captured in the reference model. Overall, RRE enables the automatic improvement of de novo repeat libraries and the reconstruction of highly degenerate and fragmented repeats.

bioinformatics↗

bioRxiv2025

AXL governs axolotl cardiac regeneration and directs mammalian cardiomyocyte dedifferentiation

Cardiac injury outcomes vary widely across species, from complete regeneration to irreversible scarring. Using single-nucleus multiomics and spatial transcriptomics, we generated a spatially resolved atlas of axolotl heart regeneration following injury, identifying a distinct border-zone cardiomyocyte population with a pro-regenerative transcriptional program. Ligand-receptor analysis of the border zone niche identified enrichment of the receptor tyrosine kinase AXL in injury-responsive cardiomyocytes and its ligand Gas6 in endothelial cells. Functional perturbation demonstrated AXL requirement for border-zone cardiomyocyte activation and axolotl heart regeneration. In murine cardiomyocytes, AXL overexpression induced sarcomere disassembly, metabolic rewiring, and immature gene expression without triggering proliferation. These findings show that AXL signaling induces cardiomyocyte dedifferentiation and uncouples dedifferentiation from cell cycle re-entry, providing mechanistic insight into cellular plasticity during heart regeneration.

cell biology↗

bioRxiv2025

Divergent stem cell mechanisms governing the primary body axis and appendage regeneration in the axolotl

Exploring the fundamental mechanisms of organ regeneration is crucial for advancing regenerative medicine. The axolotl tail represents a unique opportunity to study regeneration of the primary axis including segmented muscle, vertebrae and skin. During tail development, muscle stem cells (MuSCs) displayed expected specificity to the muscle lineage. Tail amputation, however, induced expansion of MuSC potential yielding clonal contribution to muscle, connective tissue including cartilage, pericytes, and fibroblasts. This expanded potential was not observed during limb regeneration, and cross-transplantation showed these differences in potential are intrinsic. ScRNA-Seq profiling revealed that tail MuSCs revert to an embryonic mesoderm-like state. Through genetic manipulation involving the over-expression of constitutively active TGF-{beta} receptors or Smad7 (antagonist of TGF-{beta} signaling) in MuSCs, we demonstrated that the levels of TGF-{beta} signal determine the fate outcome of MuSCs to connective tissue lineage or muscle respectively. Our findings illustrate a fundamental difference between regeneration of primary axis versus limb and offers a novel stem cell source for regeneration of axial skeletal tissues.

developmental biology↗

bioRxiv2024

From naïve pluripotency to human neural organoids through a three-dimensional morphogenetic continuum

Human central nervous system (CNS) development involves complex transitions from pluripotency to regionalised neural tissues. The early phases of this process are inaccessible in humans but can potentially be modelled in vitro using brain organoids, including to study neurodevelopmental disorders. However, current methods are based on post-implantation-like human pluripotent stem cells (hPSCs), which exhibit a hypermethylated state and show epigenetic memory retention. Here we developed a 3D model of human CNS development, starting from naive human induced PSCs (hiPSCs), which exhibit a hypomethylated pre-implantation-like state of pluripotency and develop into 3D neuroepithelial cysts in a timely morphogenetic continuum. Upon treatment with appropriate signalling cues, naive-derived neuroepithelial cysts can be specified toward different axial identities. Extended culture of anterior-specified organoids results in forebrain-like structures containing both dorsal and ventral neural precursors as well as mature neurons, exhibiting appropriate cellular diversity and functional properties. We applied this system to model Fragile X Syndrome (FXS), an epigenetically regulated neurodevelopmental disorder. We found that FXS patient-derived naive hiPSCs, initially demethylated at the Fmr1 locus, gradually underwent remethylation during organoid development. In addition, Fmr1 silencing started much earlier than can be detected by pre-natal analysis, and is concomitant with the development of mosaicisms. Our approach provides a new platform for studying human CNS development, including early epigenetic events and regional patterning, demonstrating the potential of naive hiPSC-derived organoids for modelling neurodevelopmental disorders with complex epigenetic regulation. Highlights- single naive hiPSCs differentiate into 3D neuroepithelial cysts in a timely morphogenetic continuum - signalling cues at appropriate developmental transitions can direct naive hiPSC- derived organoids to different regional identities of the human CNS - naive hiPSC-derived forebrain organoids display cellular complexity representing both dorsal and ventral identities - forebrain organoids from Fragile X Syndrome patients recapitulate the genetic instability and epigenetic dysregulation of Fmr1 locus.

cell biology↗

bioRxiv2024

Neural tube organoid generation: a robust and reproducible protocol from single mouse embryonic stem cells

The development of mammals is a highly complex process, characterized by the necessity for precise concentration- and time-dependent signaling for correct pattern formation and morphogenesis. Despite considerable technological advancements and knowledge gathered, numerous aspects of mammalian development remain elusive. When examining the entire organism, it becomes challenging to disentangle the effects of individual pathways or the mechanism by which external stimuli guide the interference of surrounding tissues and factors. In addressing this complexity, three-dimensional (3D) in vitro models such as organoids have emerged as valuable tools. Organoids, derived from embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs), exhibit tissue-like features that closely resemble their in vivo counterparts in terms of expression patterns and functionality. Importantly, they offer accessibility for manipulation and extensive biological studies within a controlled experimental setting. Despite originating from pluripotent cultures, organoid systems often exhibit heterogeneity and substantial variability, limiting their utility when studying complex and intricate biological questions. Therefore, there is a pressing need for detailed protocols aimed at harmonizing procedures that result in high-quality reproducible data, reduction of materials used and which importantly permit the investigation of convoluted phenomena. In this context, we present an optimized protocol for the cultivation of neural tube organoids (NTOs) in vitro. By producing stable culture conditions and offering comprehensive troubleshooting strategies, this protocol enables the reliable and reproducible generation of NTOs which serve as an adequate model to study relevant scientific questions. SUMMARYThree-dimensional neural tube organoids (NTOs) derived from mouse embryonic stem cells are valuable tools to study the central nervous system during early development. Here, we present a step-by-step demonstration of an optimized protocol for cultivating NTOs in vitro, providing stable culture conditions and troubleshooting strategies for reliable and reproducible NTO generation.

developmental biology↗

bioRxiv2024

Lineage tracing of Shh+ floor plate cells and dynamics of dorsal-ventral gene expression in the regenerating axolotl spinal cord

Both development and regeneration depend on signalling centres, which are sources of locally secreted tissue-patterning molecules. As many signalling centres are decommissioned before the end of embryogenesis, a fundamental question is how signalling centres can be re-induced later in life to promote regeneration after injury. Here, we use the axolotl salamander model (Ambystoma mexicanum) to address how the floor plate is assembled for spinal cord regeneration. The floor plate is an archetypal vertebrate signalling centre that secretes Shh ligand and patterns neural progenitor cells during embryogenesis. Unlike mammals, axolotls continue to express floor plate genes (including Shh) and downstream dorsal-ventral patterning genes in their spinal cord throughout life, including at steady state. The parsimonious hypothesis that Shh+ cells give rise to functional floor plate cells for regeneration had not been tested. Using HCR in situ hybridisation and mathematical modelling, we first quantitated the behaviours of dorsal-ventral spinal cord domains, identifying significant increases in gene expression level and floor plate size during regeneration. Next, we established a transgenic axolotl to specifically label and fate map Shh+ cells in vivo. We found that labelled Shh+ cells gave rise to regeneration floor plate, and not to other neural progenitor domains, after tail amputation. Thus, despite changes in domain size and downstream patterning gene expression, Shh+ cells retain their floor plate identity during regeneration, acting as a stable cellular source for this regeneration signalling centre in the axolotl spinal cord.

developmental biology↗

bioRxiv2024

The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes

Many animal genomes are characterized by highly conserved chromosomal homologies that pre-date the ancient origin of this clade. Despite such conservation, the evolutionary forces behind the retention, expansion, and contraction of chromosomal elements, and the resulting macro-evolutionary implications, are unknown. Here we present a comprehensive stem-cell resolved genomic and transcriptomic study of the fresh-water cnidarian Hydra, an animal characterized by its high regenerative capacity, the ability to propagate clonally, and an apparent lack of aging. Using single-haplotype telomere-to-telomere genome assemblies of two recently diverged hydra strains, we show how the macro-evolutionary history of chromosomal elements is shaped by both old and recent transposable element (TE) expansions. Unique features of hydra biology allowed us to compare the individual genomes of hydras three stem cell lineages. We show that distinct TE families are active at both transcriptional and genomic levels via non-random insertions in the genomes of each of these lineages. In transcriptomes, over 14,000 transcripts were composed of nearly complete TE sequences, and further classification into families, subfamilies, and individual loci reveals cell type-specific TE expression. The active TEs include elements that differentially contribute to changes in the genome size as well as persistent structural variants around loci associated with cell proliferation. Our study reveals 14 active TE families that primarily act in this role and are predominantly composed of DNA elements. Evolutionary analysis revealed that these families constitute a highly conserved TE core in eukaryotic and metazoan genomes. Our results suggest an ancient role for these core TEs as self-renewing genomic components that persist beyond ancient chromosomal homologies.

genomics↗

bioRxiv2024

Adeno-associated viruses for efficient gene expression in the axolotl nervous system

Axolotls are models for studying nervous system evolution, development, and regeneration. Tools to visualize and manipulate cells of the axolotl nervous system with high efficiency, spatial and temporal precision are therefore greatly required. Recombinant adeno-associated viruses (AAVs) are frequently used for in vivo gene transfer of the nervous system but virus-mediated gene delivery to the axolotl nervous system has not yet been described. Here, we demonstrate the use of AAVs for efficient gene transfer within the axolotl brain and the retina. We show that serotypes AAV8, AAV9, AAVRG and AAVPHP.eB are suitable viral vectors to infect both excitatory and inhibitory neuronal populations of the axolotl brain. We further use AAV9 to trace retrograde and anterograde projections between the retina and the brain and identify a cell population projecting from the brain to the retina. Together, our work establishes AAVs as a powerful tool to interrogate neuronal organization in the axolotl.

neuroscience↗

bioRxiv2024

Somite-independent regeneration of the axolotl primary body axis

Primary body-axis development is a highly conserved process that proceeds through somitogenesis and subsequent subdivision into dermatome, myotome, and sclerotome. Defects in somitic-clock genes such as Hes7 lead to vertebral-segmentation defects in mice and fish. Here we show that in the axolotl, although Hes7 is necessary for proper embryonic vertebral segmentation, it is-- surprisingly--dispensable during tail regeneration. We investigated the mechanism of vertebral segmentation during regeneration which initially occurs through extension of a cartilage rod ventral to the spinal cord. We find that the regenerating cartilage rod undergoes a periodic wrinkling that provides a template for vertebral segmentation. Via direct mechanical measurements and biophysical perturbations, we show that a model of compression-induced buckling instability can predict vertebral segmentation. The cartilage rod and other somitic derivatives (muscle, cartilage, tendon, fibroblasts) arise from tendon-like, Lfng+ multi-potent mesenchymal progenitors, which display a gene regulatory state distinct from somitic progenitors. In summary, we uncover a mechanism of vertebral segmentation during axolotl tail regeneration that is distinct from the somite-based developmental mechanism.

developmental biology↗

bioRxiv2023

Molecular basis for positional memory and its reprogrammability in limb regeneration

Upon limb amputation in salamanders, anterior and posterior connective tissue cells form distinct signalling centres that together fuel successful regeneration. The molecular properties that distinguish anterior and posterior cells prior to injury, which enable them to initiate different signalling centres after amputation, are not known. These anterior and posterior identities, crucial for regeneration, were thought to be established during development and to persist through successive regeneration cycles as positional memory. However, the molecular nature of these memory states and whether these identities can be engineered have remained outstanding questions. Here, we identify a positive feedback mechanism encoding posterior identity in the axolotl limb, which can be used to newly encode positional memory in regenerative cells. Posterior cells express residual levels of the bHLH transcription factor Hand2 from development and this is a priming molecule necessary and sufficient to establish a Shh signalling centre after limb amputation. During regeneration, Shh feeds back and reinforces Hand2 expression in nearby cells. Hand2 is sustained following regeneration, safeguarding posterior memory, while Shh is shut off. As a consequence of this Hand2-Shh system, anterior and posterior identities are differentially susceptible to alteration. Posterior cells are stabilised against anteriorisation as their expression of Hand2 poises them to trigger the Hand2-Shh loop. In contrast, anterior cells can be reprogrammed: a transient exposure to Shh during regeneration causes anterior cells to gain Hand2 expression and a lasting competence to express Shh. In this way, regeneration is an opportunity and entry point to re-write positional memory. Our results implicate positive feedback in the stability of positional memory and explain why positional memory is more easily altered in one direction (anterior to posterior) than the other. Because modifying positional memory changes signalling outputs from regenerative cells, our findings have wider implications for tissue engineering.

developmental biology↗

bioRxiv2023

Clonal neural tube organoids self-organise floorplate through BMP-mediated cluster competition

The neural tube (NT) has been a hallmark example of embryonic induction and patterning whereby the notochord induces an organiser, the floorplate, that secretes Sonic Hedgehog (SHH) to pattern the surrounding field of neural progenitors. On the other hand, NT organoids (NTOs) formed from embryonic stem cells (ESCs) undergo spontaneous floorplate formation and patterning in the absence of their normal embryonic inducers. Understanding how stem cells undergo regulative organiser formation is a central challenge in biology. Here, we investigated the self-organisation of a SHH-expressing floorplate organiser using clonal NTOs. Expression of FOXA2, a floorplate transcription factor, was initially spatially scattered before resolving into multiple clusters. These FOXA2+ clusters underwent competition and physical sorting, resulting in a stable "winning" floorplate. We identified BMP signalling as a key governor of long-range cluster competition. FOXA2+ clusters expressed BMP4 ligand suppressing FOXA2 in receiving cells, while simultaneously expressing the BMP-inhibitor NOGGIN to secure FOXA2+ cluster survival. Genetic mutation of Noggin perturbed the floorplate not only in NTOs but also in vivo at the mid-hindbrain region of the mouse NT. These results demonstrate how the floorplate can form autonomously without its well-known inducer, the notochord, suggesting redundant mechanisms ensuring robustness. Defining molecular pathways that govern organiser self-organisation is critical in harnessing the developmental plasticity of stem cells toward directed tissue engineering.

developmental biology↗

bioRxiv2023

Circuit to target approach defines an autocrine myofibroblast loop that drives cardiac fibrosis

Fibrosis is a broad pathology of excessive scarring with substantial medical implications. The fibrotic scar is produced by myofibroblasts that interact with macrophages. Fibrosis is a complex process involving thousands of factors, therefore, to better understand fibrosis and develop new therapeutic approaches, it is necessary to simplify and clarify the underlying concepts. Recently, we described a mathematical model for a macrophage-myofibroblast cell circuit, predicting two types of fibrosis - hot fibrosis with abundant macrophages and myofibroblasts, and cold fibrosis dominated by myofibroblasts alone. To test these concepts and intervention strategies in a medically relevant system, we use a widely studied in-vivo injury model for fibrosis, myocardial infarction (MI). We show that cold fibrosis is the final outcome of MI in both mice and pigs and demonstrate that fibrosis can shift toward healing in regenerative settings. MI begind with an increase of myofibroblasts and macrophages, followed by macrophage decline leading to persistent cold fibrosis (only myofibroblasts). During this process, fibroblasts, unlike macrophages, acquire distinct fate changes. Using mathematical modeling we predict that targeting of the autocrine signal for myofibroblast division could block cold fibrosis. We identify TIMP1 as an autocrine cardiac myofibroblast growth factor in-vitro. Treatment of adult mice after MI with anti-TIMP1 antibodies reduces fibrosis in-vivo. This study shows the utility of the concepts of hot and cold fibrosis and the feasibility of our circuit-to-target approach to reduce fibrosis after acute cardiac injury by inhibiting the myofibroblast autocrine loop.

systems biology↗

bioRxiv2022

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration

The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed "positional information". How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program.

developmental biology↗

bioRxiv2022

Canonical Wnt Signaling and the Regulation of Divergent Mesenchymal Fgf8 expression in Axolotl Limb Development and Regeneration

The expression of Fibroblast growth factors (Fgf) ligands in a specialized epithelial compartment, the Apical Ectodermal Ridge (AER), is a conserved feature of limb development across vertebrate species. In vertebrates, Fgf 4, 8, 9, and 17 are all expressed in the AER. An exception to this paradigm is the salamander (axolotl) developing and regenerating limb, where key Fgf ligands are expressed in the mesenchyme. The mesenchymal expression of Amex.Fgf8 in axolotl has been suggested to be critical for regeneration. To date, there is little knowledge regarding what controls Amex.Fgf8 expression in the axolotl limb mesenchyme. A large body of mouse and chick studies have defined a set of transcription factors and canonical Wnt signaling as the main regulators of epidermal Fgf8 expression in these organisms. In this study, we address the hypothesis that alterations to one or more of these components during evolution has resulted in mesenchymal Amex.Fgf8 expression in the axolotl. To sensitively quantify gene expression with spatial precision, we combined optical clearing of whole-mount axolotl limb tissue with single molecule fluorescent in situ hybridization and a semi-automated quantification pipeline. Several candidate upstream components were found expressed in the axolotl ectoderm, indicating that they are not direct regulators of Amex.Fgf8 expression. We found that Amex.Wnt3a is expressed in axolotl limb epidermis, similarly to chicken and mouse. However, unlike in amniotes, Wnt target genes are activated preferentially in limb mesenchyme rather than in epidermis. Inhibition and activation of Wnt signaling results in downregulation and upregulation of mesenchymal Amex.Fgf8 expression respectively. These results implicate a shift in tissue responsiveness to canonical Wnt signaling from epidermis to mesenchyme as one step contributing to the unique mesenchymal Amex.Fgf8 expression seen in the axolotl.

developmental biology↗

bioRxiv2022

Single-cell analyses of axolotl forebrain organization, neurogenesis, and regeneration

Salamanders are important tetrapod models to study brain organization and regeneration, however the identity and evolutionary conservation of brain cell types is largely unknown. Here, we delineate cell populations in the axolotl telencephalon during homeostasis and regeneration, representing the first single-cell genomic and spatial profiling of an anamniote tetrapod brain. We identify glutamatergic neurons with similarities to amniote neurons of hippocampus, dorsal and lateral cortex, and conserved GABAergic neuron classes. We infer transcriptional dynamics and gene regulatory relationships of postembryonic, region-specific direct and indirect neurogenesis, and unravel conserved signatures. Following brain injury, ependymoglia activate an injury-specific state before reestablishing lost neuron populations and axonal connections. Together, our analyses yield key insights into the organization, evolution, and regeneration of a tetrapod nervous system.

developmental biology↗