Biology subjects

Schier, A. F.

Publications and source records attributed to Schier, A. F..

At least 19 recordsLinked to original sources

bioRxiv2026

Transcriptional subtypes, anatomical organization, and sexual dimorphism of sensory vagus neurons in Danionella cerebrum

Visceral sensory neurons sense and modulate the brain, behavior, and the internal organs. However, these neurons have been difficult to study comprehensively due to their projections deep within the body. Here, we establish the transparent miniature fish Danionella cerebrum as a model for studying the sensory vagus nerve in an adult vertebrate. By generating a transgenic line to label D. cerebrum cranial sensory ganglia, we were able to both anatomically characterize and transcriptionally profile the sensory vagus at single-cell resolution. Anatomically, we find that the vagal ganglia have a somatotopic layout. Transcriptionally, the sensory vagus is comprised of diverse sensory subtypes conserved with other vertebrates, including nutrient-sensing, mechanoreceptive, nociceptive, and thermosensitive subtypes, as well as polymodal combinations. Visualizing subtype marker genes identified somatotopic-specific sensory subtypes. Notably, the D. cerebrum sensory vagus is not static across development: it becomes anatomically sexually dimorphic during sexual maturation and undergoes continuous adult neurogenesis. The molecular and anatomical atlas of the sensory vagus lays the foundation for functional studies of body-brain communication in D. cerebrum.

neuroscience↗

bioRxiv2026

Odor preference maps to cohesive transcriptional domains in the olfactory bulb

Animals classify odors along behaviorally relevant dimensions, yet how the olfactory bulb, the first stage of olfactory processing, is organized and how this organization relates to odor classification remains unclear. Here, we identify cohesive transcriptional domains within the larval zebrafish olfactory bulb whose differential functional recruitment reflects odor preference. Using a flow-based two-choice assay, we characterized behavioral preferences across chemically diverse odors. Mapping odor-evoked neuronal activity patterns revealed that similarly preferred odors converge onto shared spatial activation patterns in the olfactory bulb. Whole-mount multiplexed spatial transcriptomics revealed that projection neuron and interneuron subtypes form cohesive spatial domains. Mapping odor-activated neurons onto these domains identified preference-biased recruitment of specific neuronal subtypes. Targeted ablation of a TH+ interneuron population associated with attraction selectively impaired attraction while sparing aversion. Together, these findings reveal that the olfactory bulb is organized into spatially cohesive, transcriptionally defined domains and that selective recruitment of specific subtypes is linked to odor preference. Key findingsO_LIChemically diverse odorants elicit behaviors reflecting olfactory preference. C_LIO_LITranscriptionally defined neuronal subtypes form cohesive spatial domains in the olfactory bulb. C_LIO_LIOdorants of opposing preference recruit distinct transcriptional domains in the olfactory bulb. C_LIO_LIA TH+ interneuron population is selectively required for odor attraction but not aversion. C_LI

neuroscience↗

bioRxiv2026

High-Fidelity Long-term Whole-embryo Lineage and Fate Reconstruction by Iterative Tracking with Error Correction

Reconstructing the complete cell lineages and fate maps of a living embryo has remained a central challenge in developmental biology. Here we introduce ITEC (Iterative Tracking with Error Correction), a fully unsupervised method that automatically reconstructs the lineage of every cell in the embryo with high fidelity. ITEC was validated with manually annotated lineages on four cross-species datasets including zebrafish, mouse, and Drosophila. We reconstructed the developmental lineages of a zebrafish embryo from terabyte-scale data of total 18.5 million cells with an estimated accuracy of over 99.7%. With ITEC, we revealed spatiotemporal dynamics of key morphogenetic processes such as somite boundary formation, demonstrated the various patterns of spatial sorting among adjacent organs or anatomical regions, and identified associations between cellular movement and spatial transcriptomics. ITEC provides a powerful platform for retrospective fate mapping and systematic exploration of developmental dynamics at the cellular scale and single-embryo level.

bioinformatics↗

bioRxiv2025

The mechanosensory DEG/ENaC channel DEGT-1 is a proprioceptor of C. elegans foregut movement

The gastrointestinal tract is subjected to extensive mechanosensory stimulation during food ingestion. However, the identities of mechanosensory receptors in the enteric nervous system are largely unknown. The pharynx of C. elegans is a structurally and functionally homologous model of the vertebrate foregut, but is comprised of only 20 neurons that are embedded within the muscles and epithelial cells of the organ. Here we report that the DEG/ENaC family ion channel DEGT-1 is a proprioceptor of pharynx movement. DEGT-1 protein is expressed in 4 pharyngeal neurons (MI, M3, I4, and M5) and localized to their neuronal soma in direct contact with the collagenous pharyngeal basement membrane. degt-1 mutants display abnormally rapid feeding in the presence of food, causing global changes in lipid accumulation. degt-1 mutants also pump rapidly when pumping is induced by the presence of serotonin alone, suggesting that DEGT-1 is required for proprioception of pharyngeal pumping itself, rather than sensing ingested food. DEGT-1 is required in only two pharyngeal neurons (I4 and M5) to control pumping rate. Taken together, these results suggest that DEGT-1 modulates pharyngeal pumping rate by relaying proprioceptive feedback generated by the shear force of the pharynx against its own basement membrane. Thus, mechanosensors in enteric nervous systems modulate organ function not only by detecting forces from ingested contents, but also the movements of the organ itself.

neuroscience↗

bioRxiv2024

Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis

Spatiotemporal patterns of gene expression underlie embryogenesis. Despite progress in single-cell genomics, mapping these patterns across whole embryos with comprehensive gene coverage and at high resolution has remained elusive. Here, we introduce a whole-embryo imaging platform using multiplexed error-robust fluorescent in-situ hybridization (weMERFISH). We quantified the expression of 495 genes in whole-mount zebrafish embryos at subcellular resolution. Integration with single-cell multiomics data generated an atlas detailing the expression of 25,872 genes and the accessibility of 294,954 chromatin regions, explorable with an online interface MERFISHEYES (beta version). We found that temporal gene expression aligns with cellular maturation and morphogenetic movements, diverse expression patterns correspond to composites of tissue-specific accessible elements, and changes in gene expression generate sharp boundaries during gastrulation. These results establish a novel approach for whole-organism spatial transcriptomics, provide a comprehensive spatially resolved atlas of gene expression and chromatin accessibility, and reveal the diversity, precision and emergence of embryonic patterns.

developmental biology↗

bioRxiv2024

Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis

The interplay between transcription factors and chromatin accessibility regulates cell type diversification during vertebrate embryogenesis. To systematically decipher the gene regulatory logic guiding this process, we generated a single-cell multi-omics atlas of RNA expression and chromatin accessibility during early zebrafish embryogenesis. We developed a deep learning model to predict chromatin accessibility based on DNA sequence and found that a small number of transcription factors underlie cell-type-specific chromatin landscapes. While Nanog is well-established in promoting pluripotency, we discovered a new function in priming the enhancer accessibility of mesendodermal genes. In addition to the classical stepwise mode of differentiation, we describe instant differentiation, where pluripotent cells skip intermediate fate transitions and terminally differentiate. Reconstruction of gene regulatory interactions reveals that this process is driven by a shallow network in which maternally deposited regulators activate a small set of transcription factors that co-regulate hundreds of differentiation genes. Notably, misexpression of these transcription factors in pluripotent cells is sufficient to ectopically activate their targets. This study provides a rich resource for analyzing embryonic gene regulation and reveals the regulatory logic of instant differentiation.

developmental biology↗

bioRxiv2024

Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes

The partitioning of ecological niches is a fundamental component of species diversification in adaptive radiations. However, it is presently unknown if and how such bursts of organismal diversity are influenced by temporal niche partitioning, wherein species avoid competition by being active during different time windows. Here, we address this question through profiling temporal activity patterns in the exceptionally diverse fauna of cichlid fishes from African Lake Tanganyika. By integrating week-long longitudinal behavioural recordings of over 500 individuals from 60 species with eco-morphological and genomic information, we provide two lines of evidence that temporal niche partitioning facilitated this massive adaptive radiation. First, Tanganyikan cichlids exhibit all known circadian temporal activity patterns (diurnal, nocturnal, crepuscular, and cathemeral) and display substantial inter-specific variation in daily amounts of locomotion. Second, many species with similar habitat and diet niches occupy distinct temporal niches. Moreover, our results suggest that shifts between diurnal and nocturnal activity patterns are facilitated by a crepuscular intermediate state. In addition, genome-wide association studies indicate that the genetics underlying activity patterns is complex, with different clades associated with different combinations of variants. The identified variants were not associated with core circadian clock genes but with genes implicated in synapse function. These observations indicate that temporal niche partitioning contributed to adaptive radiation in cichlids and that many genes are associated with the diversity and evolution of temporal activity patterns.

evolutionary biology↗

bioRxiv2024

Optogenetic control of Nodal signaling patterns

A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embryonic cells decode these signals to make appropriate fate decisions. Here, we present new optogenetic reagents and an experimental pipeline for creating designer Nodal signaling patterns in live zebrafish embryos. Nodal receptors were fused to the light-sensitive heterodimerizing pair Cry2/CIB1N, and the Type II receptor was sequestered to the cytosol. The improved optoNodal2 reagents eliminate dark activity and improve response kinetics, without sacrificing dynamic range. We adapted an ultra-widefield microscopy platform for parallel light patterning in up to 36 embryos and demonstrated precise spatial control over Nodal signaling activity and downstream gene expression. Patterned Nodal activation drove precisely controlled internalization of endodermal precursors. Further, we used patterned illumination to generate synthetic signaling patterns in Nodal signaling mutants, rescuing several characteristic developmental defects. This study establishes an experimental toolkit for systematic exploration of Nodal signaling patterns in live embryos.

developmental biology↗

bioRxiv2023

Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion

During differentiation, cells become structurally and functionally specialized, but comprehensive views of the underlying remodeling processes are elusive. Here, we leverage scRNA-seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system - the zebrafish notochord and hatching gland. First, we present an approach to integrate expression and functional similarities for gene module identification, revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second, we focused on the unfolded protein response (UPR) transducer module to study how general versus cell-type specific secretory functions are regulated. By profiling loss- and gain-of-function embryos, we found that the UPR transcription factors creb3l1, creb3l2, and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program, while xbp1 partners with bhlha15 to activate a gland-specific secretion program. Our study offers a multi-source integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions.

developmental biology↗

bioRxiv2023

The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis

The 5' UTRs of mRNAs are critical for translation regulation, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR is sufficient to confer temporal dynamics to translation initiation, and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, DaniO5P, revealed a combined role for 5' UTR length, translation initiation site context, upstream AUGs and sequence motifs on in vivo ribosome recruitment. DaniO5P predicts the activities of 5' UTR isoforms and indicates that modulating 5' UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5' UTR-based translation regulation in early vertebrate development and lays the foundation for identifying the underlying molecular effectors. HighlightsO_LIIn vivo MPRA systematically interrogates the regulatory potential of endogenous 5' UTRs C_LIO_LIThe 5' UTR alone is sufficient to regulate the dynamics of ribosome recruitment during early embryogenesis C_LIO_LIThe MPRA identifies 5' UTR cis-regulatory motifs for translation initiation control C_LIO_LI5' UTR length, upstream AUGs and motif grammar contribute to the differential regulatory capability of 5' UTR switching isoforms C_LI

developmental biology↗

bioRxiv2023

Frequent transitions from night-to-day activity after mass extinctions

Why certain species survive large-scale extinction events while others do not is poorly understood. While the fossil record can provide insights into morphological adaptations that increase survival probabilities, it provides limited information regarding behavioural traits. Here we integrate behavioural data with phylogenetic comparative models to study the evolution of day-night activity patterns (nocturnality and diurnality) in bony fishes, which have persisted through the last four mass extinction events. Our findings in fish, combined with data across all other clades of vertebrates, provide four lines of evidence that nocturnality conferred an evolutionary advantage during mass extinctions, and that frequent nocturnal-to-diurnal transitions facilitated post-extinction diversification: First, phylogenetic reconstruction indicates that the last common ancestors of all vertebrates and of clades of bony vertebrates were nocturnal. Second, in the lineage of bony fishes, which contains over half of all vertebrate species, twice as many transitions between nocturnal and diurnal activity patterns have occurred compared to tetrapods. Third, within a specific ecological niche, different species exhibit distinct temporal activity patterns, suggesting widespread temporal niche partitioning. Fourth, independent bursts in night-to-day transitions followed large-scale extinction events during the last two geological eras in all four major bony vertebrate groups. These observations suggest that ancestral nocturnality and frequent transitions to diurnality helped vertebrates survive and diversify in the face of extinction events, such as those expected during the current "6th mass extinction" event caused by anthropogenic climate change.

evolutionary biology↗

bioRxiv2023

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.

developmental biology↗

bioRxiv2021

Regulation of Vg1 biogenesis during mesendoderm induction

The TGF-beta signals Vg1 (Dvr1/Gdf3) and Nodal form heterodimers to induce vertebrate mesendoderm. The Vg1 proprotein is a monomer retained in the endoplasmic reticulum (ER) and is processed and secreted upon heterodimerization with Nodal, but the mechanisms underlying Vg1 biogenesis are largely elusive. Here we clarify the mechanisms underlying Vg1 retention, processing, secretion and signaling, and introduce a Synthetic Processing (SynPro) system that enables the programmed cleavage of ER-resident and extracellular proteins. First, we find that Vg1 can be processed by intra- or extracellular proteases. Second, Vg1 can be processed without Nodal but requires Nodal for secretion and signaling. Third, Vg1-Nodal signaling activity requires Vg1 processing, whereas Nodal can remain unprocessed. Fourth, Vg1 employs exposed cysteines, glycosylated asparagines, and BiP chaperone-binding motifs for monomer retention in the ER. These observations suggest two mechanisms for rapid mesendoderm induction: chaperone-binding motifs help store Vg1 as an inactive but ready-to-heterodimerize monomer in the ER, and the flexibility of Vg1 processing location allows efficient generation of active heterodimers both intra- and extracellularly. These results establish SynPro as a new in vivo processing system and define molecular mechanisms and motifs that facilitate the generation of active TGF-beta heterodimers. SignificanceThe TGF-beta family members Nodal and Vg1 are the major inducers of mesendoderm formation during vertebrate embryogenesis. We previously established that the Vg1 proprotein is retained in the endoplasmic reticulum (ER), and that Nodal and Vg1 form heterodimers to pattern the early embryo. However, the mechanisms underlying the retention, processing, secretion, and signaling of Vg1 have been unclear. We found two mechanisms that embryos use to efficiently generate active Nodal-Vg1 heterodimers: (1) Vg1 employs its chaperone-binding motifs to ensure its retention as a ready-to-heterodimerize monomer in the ER; (2) Using a newly devised Synthetic Processing (SynPro) System, we found that Vg1 must be processed for signaling to occur, but its processing location is flexible.

developmental biology↗

bioRxiv2020

Gene family evolution underlies cell type diversification in the hypothalamus of teleosts

Hundreds of cell types form the vertebrate brain, but it is largely unknown how similar these cellular repertoires are between or within species, or how cell type diversity evolves. To examine cell type diversity across and within species, we performed single-cell RNA sequencing of [~]130,000 hypothalamic cells from zebrafish (Danio rerio) and surface- and cave-morphs of Mexican tetra (Astyanax mexicanus). We found that over 75% of cell types were shared between zebrafish and Mexican tetra, which last shared a common ancestor over 150 million years ago. Orthologous cell types displayed differential paralogue expression that was generated by sub-functionalization after genome duplication. Expression of terminal effector genes, such as neuropeptides, was more conserved than the expression of their associated transcriptional regulators. Species-specific cell types were enriched for the expression of species-specific genes, and characterized by the neo-functionalization of members of recently expanded or contracted gene families. Within species comparisons revealed differences in immune repertoires and transcriptional changes in neuropeptidergic cell types associated with genomic differences between surface- and cave-morphs. The single-cell atlases presented here are a powerful resource to explore hypothalamic cell types, and reveal how gene family evolution and the neo- and sub-functionalization of paralogs contribute to cellular diversity.

cell biology↗

bioRxiv2019

The pattern of Nodal morphogen signaling is shaped by co-receptor expression

Embryos must communicate instructions to their constituent cells over long distances. These instructions are often encoded in the concentration of signals called morphogens. In the textbook view, morphogen molecules diffuse from a localized source to form a concentration gradient, and target cells adopt fates by measuring the local morphogen concentration. However, natural patterning systems often incorporate numerous co-factors and extensive signaling feedback, suggesting that embryos require additional mechanisms to generate signaling patterns. Here, we examine the mechanisms of signaling pattern formation for the mesendoderm inducer Nodal during zebrafish embryogenesis. We find that Nodal signaling activity spans a normal range in the absence of signaling feedback, suggesting that diffusion is sufficient for Nodal gradient formation. We further show that the range of endogenous Nodal ligands is set by the EGF-CFC co-receptor Oep: in the absence of Oep, Nodal ligands spread to form a nearly uniform distribution throughout the embryo. In turn, increasing Oep levels sensitizes cells to Nodal ligands. We recapitulate these experimental results with a computational model in which Oep regulates the diffusive spread of Nodal ligands by setting the rate of capture by target cells. This model predicts, and we confirm in vivo, the surprising observation that a failure to replenish Oep during patterning transforms the Nodal signaling gradient into a travelling wave. These results reveal that patterns of Nodal morphogen signaling are shaped by co-receptor-mediated restriction of ligand spread and cell sensitization.

developmental biology↗

bioRxiv2019

Emergence of neuronal diversity during vertebrate brain development

Neurogenesis in the vertebrate brain comprises many steps ranging from the proliferation of progenitors to the differentiation and maturation of neurons. Although these processes are highly regulated, the landscape of transcriptional changes and progenitor identities underlying brain development are poorly characterized. Here, we describe the first developmental single-cell RNA-seq catalog of more than 200,000 zebrafish brain cells encompassing 12 stages from 12 hours post-fertilization to 15 days post-fertilization. We characterize known and novel gene markers for more than 800 clusters across these timepoints. Our results capture the temporal dynamics of multiple neurogenic waves from embryo to larva that expand neuronal diversity from [~]20 cell types at 12 hpf to [~]100 cell types at 15 dpf. We find that most embryonic neural progenitor states are transient and transcriptionally distinct from long-lasting neural progenitors of post-embryonic stages. Furthermore, we reconstruct cell specification trajectories for the retina and hypothalamus, and identify gene expression cascades and novel markers. Our analysis reveal that late-stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo, while hypothalamic neural progenitors become progressively distinct with developmental time. These data provide the first comprehensive single-cell transcriptomic time course for vertebrate brain development and suggest distinct neurogenic regulatory paradigms between different stages and tissues.

developmental biology↗

bioRxiv2018

Distributed plasticity drives visual habituation learning in larval zebrafish

Habituation is a simple form of learning, where animals learn to reduce their responses to repeated innocuous stimuli. While habituation is simple in concept, its exact implementation in the vertebrate brain is not clear. It could occur via a single plasticity event at a singular site in the circuit, or alternatively via more complex strategies that combine multiple mechanisms at various processing stages and sites. Here, we use a visual habituation assay in larval zebrafish, where larvae habituate to sudden reductions in illumination (dark flashes). We find that 8 different components of this response habituate, including the probability of executing a response, its latency, and measures of its magnitude. Through behavioural analyses, we find that habituation of these different behavioural components occurs independently of each other and at different locations in the circuit. Further, we use genetic and pharmacological manipulations to show that habituation of different behavioural components are molecularly distinct. These results are consistent with a model by which visual habituation originates from the combination of multiple independent processes, which each act to adapt specific components of behaviour. This may allow animals to more specifically habituate behaviour based on stimulus context or internal state.

neuroscience↗

bioRxiv2018

Convergent temperature representations in artificial and biological neural networks

While discoveries in biological neural networks (BNN) shaped artificial neural networks (ANN) it is unclear if representations and algorithms are shared between ANNs and BNNs performing similar tasks. Here, we designed and trained an ANN to perform heat gradient navigation and found striking similarities in computation and heat representation to a known zebrafish BNN. This included shared ON and OFF type representations of absolute temperature and rates of change. Importantly, ANN function critically relied on zebrafish like units. We could furthermore use the accessibility of the ANN to discover a new temperature responsive cell type in the zebrafish cerebellum. Finally, our approach generalized since training the same ANN constrained by the C. elegans motor repertoire resulted in distinct neural representations matching features observed in the worm. Together, these results emphasize convergence of ANNs and BNNs on canonical representations and that ANNs form a powerful tool to understand their biological counterparts.

neuroscience↗