Biology subjects

Schneider, I.

Publications and source records attributed to Schneider, I..

12 recordsLinked to original sources

bioRxiv2026

A conserved enhancer cluster regulates efnb2 expression in the vertebrate dorsal retina

The vertebrate retina is patterned along its dorsal-ventral (DV) axis by conserved signaling centers, yet the cis-regulatory architecture maintaining these territories remains unclear. Using the four-eyed fish Anableps anableps, which enables physical separation of dorsal and ventral retina, we integrated RNA-seq, ATAC-seq and Hi-C to map DV regulatory landscapes. We identify a 29-kb dorsal-enriched enhancer cluster within a gene poor region between efnb2a and gtpbp8, embedded in a conserved topologically associating domain spanning efnb2a-gtpbp8-slc10a2. Dorsal-biased chromatin contacts link this cluster to the efnb2a promoter. The orthologous human region contains a genome-wide significant association with retinal thickness (rs2575134; P = 2e-14). Leveraging the compact genome of Tetraodon nigroviridis, we cloned the orthologous interval and show that it drives dorsal retina-specific reporter expression in zebrafish and mouse. Together, these results identify an evolutionarily conserved regulatory domain controlling retinal axial identity and linking enhancer architecture to human ocular variation. Funding, National Science Foundation.

evolutionary biology↗

bioRxiv2026

Canonical mTOR signaling supports complete fin regeneration

The mechanistic target of rapamycin (mTOR) pathway is a deeply conserved regulator of cellular growth, metabolism, and tissue repair. In vertebrates, mTOR activity is broadly required for wound healing and regeneration. Recent work in salamanders identified unique amino acid expansions within the mTOR protein. These expansions are thought to confer hypersensitive kinase activity, which was proposed to support rapid translational activation and exceptional limb regeneration capacity. This has raised the possibility that canonical, mammalian-like mTOR signaling may be insufficient to support regeneration of complex appendages. Here, we test this hypothesis by investigating fin regeneration in the Senegal bichir (Polypterus senegalus), a ray-finned fish capable of fully regenerating fins containing bone, cartilage, muscle, and connective tissue with cellular complexity comparable to tetrapod limbs. We show that fin amputation triggers rapid activation of canonical mTOR signaling, and pharmacological inhibition of mTOR with rapamycin abolishes fin regeneration despite successful wound closure. Single-nucleus RNA sequencing (snRNA-seq) across multiple regenerative stages reveals that mTOR pathway components are selectively upregulated in proliferative epidermal and connective tissue cells, and myeloid cell populations. Rather than causing a global shutdown of gene expression, mTOR inhibition specifically dampened the induction of translational machinery and glycolytic programs, two canonical downstream outputs of mTOR signaling. In addition, myeloid cells exhibited pronounced sensitivity to mTOR inhibition, showing attenuated immune-competent and pro-regenerative programs such as interferon-associated signaling, antigen processing, and innate immune coordination. We propose that salamander-specific mTOR hypersensitivity represents an evolutionary acceleration of an ancestral regenerative program, rather than a prerequisite for limb regeneration. Significance StatementThe ability to regenerate complex appendages varies widely among vertebrates, yet the molecular basis of this variation remains poorly understood. Salamanders harbor a uniquely hypersensitive form of mTOR that has been proposed to be essential for limb regeneration. Using Polypterus fin regeneration as a model system, we demonstrate that a canonical vertebrate mTOR protein is compatible with regeneration of a complex, limb-like appendage. Our results show that mTOR acts through selective metabolic, translational, and immune programs. These findings suggest that salamander-specific mTOR hypersensitivity represents a derived enhancement rather than a condition for appendage regeneration and provide insight into the evolutionary foundations of regenerative competence.

developmental biology↗

bioRxiv2025

Aligned collagen fibers drive distinct traction force signatures to regulate contact guidance

Cellular forces on isotropically deposited extracellular matrix (ECM) have been measured extensively. However, in vivo, cells exert traction force on collagen fiber networks within ECM. Often times collagen fibers are aligned as in cancer, fibrosis and during wound healing. How forces are transmitted on aligned collagen fibers and how the cytoskeleton regulates this is unknown. Here, we develop a dual-traction force microscopy (d-TFM) approach that includes collagen fibers attached to flexible substrates with fiduciary markers on both the collagen fibers and underlying flexible substrates. This allows for the measurement of traction forces on collagen fibers in the plane of the cell, ensuring a physiologically relevant environment and accurately quantifying traction force. We find that the elastic modulus of the substrate determines the steady-state traction stress exerted by spreading cells on aligned collagen fibers, but does not affect traction force kinetics. Furthermore, collagen fiber networks on the same elastic modulus as isotropically adsorbed collagen result in higher traction stresses. Formins and Arp2/3 modulate traction stress differently, where formins affect traction stress magnitude, while Arp2/3 affects traction stress kinetics. Interestingly, we found that there is a positive correlation between traction force, migration speed and directionality on aligned collagen fibers. However, traction force does not seem to correlate with speed and directionality across distinct collagen organizational structures and across cell lines. These findings underscore the complex interplay between the mechanics of collagen fiber networks, cytoskeletal regulators and cellular traction forces, providing insights into how cells navigate complex fiber networks during migration. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/650031v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@11bb07forg.highwire.dtl.DTLVardef@e07f23org.highwire.dtl.DTLVardef@baf836org.highwire.dtl.DTLVardef@fda6ba_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Integrative multi-omics analysis of Polypterus fin regeneration reveals shared and derived fin and limb regeneration mechanisms

Comparative studies of salamander limbs and fish fins may reveal shared components of an ancestral vertebrate appendage regeneration toolkit. However, traditional fish models, such as zebrafish, regenerate only dermal fin rays, which are neither homologous to limbs nor as cellularly complex. To address this, we employed a multi-omics approach leveraging the regenerative capacity of Polypterus senegalus, a fish species capable of full fin regeneration. Single-nucleus RNA-sequencing revealed extensive erythrocyte and myeloid cell infiltration during Polypterus fin regeneration. Spatial transcriptomics identified key cellular contributors to the blastema, while cross-species comparisons with axolotl limbs uncovered both common and divergent expression patterns of wound epidermis and blastema markers. Fin amputation triggered a conserved injury response, including sequential activation of pro- and anti-inflammatory programs and DNA damage repair in cycling cells. Hypoxia responses involved hif1a modulation, consistent with other regenerative models, but uniquely included the expression of hif4a in erythrocytes and the upregulation of a myoglobin gene in the wound epidermis. Furthermore, genome-wide chromatin profiling identified candidate regeneration-responsive elements. Together, these findings establish Polypterus as a powerful comparative model for identifying shared and derived mechanisms of limb and fin regeneration.

evolutionary biology↗

bioRxiv2025

Branched and Linear F-actin Networks Control Directional Migration Switching Behavior on Aligned Collagen Fibrils

Directed cell migration is essential in many biological processes and is driven by a variety of directional cues, including aligned fibrils in the extracellular matrix (ECM), a phenomenon known as contact guidance. How different cells respond to aligned fibrils and how internal regulators like formins and Arp2/3 control contact guidance is unknown. In this study, a unique system to assemble aligned collagen fibrils on mica and to transfer them onto controllable substrates is used to probe contact guidance. This fibril alignment system reveals that cytoskeletal regulation through myosin contractility and not receptor expression drives contact guidance ability. Highly contractile cells exhibit high-fidelity contact guidance, weakly contractile cells ignore cues and moderately contractile cells use a mixture of both parallel and perpendicular migration strategies on aligned collagen fibrils. In addition to myosin contractility, formins and Arp2/3 control contact guidance in a reciprocal manner across a variety of cell types. Formins, mediators of linear F-actin structures, enhance contact guidance and Arp2/3, a mediator of branched F-actin structures, diminishes contact guidance. This controlled materials system reveals the importance of both myosin-mediated contractility as well as the antagonistic action of formins and Arp2/3 on contact guidance, providing potential targets to tune contact guidance.

bioengineering↗

bioRxiv2022

Explosive seed dispersal depends on SPL7 to ensure sufficient copper for localized lignin deposition via laccases

Exploding seed pods evolved in the Arabidopsis relative, Cardamine hirsuta, via morphomechanical innovations that allow the storage and rapid release of elastic energy. Asymmetric lignin deposition within endocarpb cell walls is one such innovation that is required for explosive seed dispersal and evolved in association with the trait. However, the genetic control of this novel lignin pattern is unknown. Here, we identify three lignin-polymerizing laccases, LAC4, 11 and 17, that precisely co-localize with, and are redundantly required for, asymmetric lignification of endocarpb cells. By screening for C. hirsuta mutants with less lignified fruit valves, we found that loss of function of the transcription factor gene SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 7 (SPL7) caused a reduction in endocarpb cell wall lignification and a consequent reduction in seed dispersal range. SPL7 is a conserved regulator of copper homeostasis and is both necessary and sufficient for copper to accumulate in the fruit. Laccases are copper-requiring enzymes. We discovered that laccase activity in endocarpb cell walls depends on the SPL7 pathway to acclimate to copper deficiency and provide sufficient copper for lignin polymerization. Hence, SPL7 links mineral nutrition to efficient dispersal of the next generation.

plant biology↗

bioRxiv2020

Non-rodent mammalian zygotes assemble dual spindles despite the presence of paternal centrosomes

The first mitosis of the mammalian embryo must partition the parental genomes contained in two pronuclei. In rodent zygotes, sperm centrosomes are degraded and, instead, acentriolar microtubule organizing centers and microtubule self-organization guide the assembly of two separate spindles around the genomes. In non-rodent mammals, including human or bovine, centrosomes are inherited from the sperm and have been widely assumed to be active. Whether non-rodent zygotes assemble a single centrosomal spindle around both genomes, or follow the dual spindle self-assembly pathway is unclear. To address this, we investigated spindle assembly in bovine zygotes by systematic immunofluorescence and real-time light-sheet microscopy. We show that two independent spindles form around the parental genomes despite the presence of centrosomes, which had little effect on spindle structure and were only loosely connected to the two spindles. We conclude that the dual spindle assembly pathway is conserved in non-rodent mammals. This could explain whole parental genome loss frequently observed in blastomeres of human IVF embryos. SummaryThis study investigates spindle assembly during the first embryonic division in bovine zygotes that, like human, inherit centrosomes from the sperm. It shows that two independent microtubule arrays form by self-organization around parental genomes with only loosely connected centrosomes.

cell biology↗

bioRxiv2020

The West African lungfish provides insights into the evolution of tetrapod tail regeneration

Salamanders, frog tadpoles, and diverse lizards have the remarkable ability to regenerate tails. Paleontological data suggests that this capacity is plesiomorphic, yet when the developmental and genetic architecture of tail regeneration arose is poorly understood. Here we show morphological and molecular hallmarks of tetrapod tail regeneration in the West African lungfish Protopterus annectens, a living representative of the sister group of tetrapods. As in salamanders, lungfish tail regeneration occurs via formation of a proliferative blastema and restores original structures, including muscle, skeleton and spinal cord. In contrast to lizards and similar to salamanders and frogs, lungfish regenerate spinal cord neurons and reconstitute dorsoventral patterning of the tail. Similar to salamander and frog tadpoles, Shh is required for lungfish tail regeneration. Through RNA-seq analysis of uninjured and regenerating tail blastema, we show that the genetic program deployed during lungfish tail regeneration maintains extensive overlap with that of tetrapods, with the upregulation of genes and signaling pathways previously implicated in amphibian and lizard tail regeneration. Furthermore, the lungfish tail blastema showed marked upregulation of genes encoding post-transcriptional RNA processing components and transposon-derived genes. Our results show that developmental processes and genetic program of tetrapod tail regeneration were present at least near the base of the sarcopterygian clade and establish the lungfish as a valuable research system for regenerative biology.

evolutionary biology↗

bioRxiv2019

von Willebrand Factor D and EGF Domains is an evolutionarily conserved and required feature of blastemas capable of multi-tissue appendage regeneration

Regenerative ability varies tremendously across species. A common feature of regeneration of appendages such as limbs, fins, antlers, and tails is the formation of a blastema--a transient structure that houses a pool of progenitor cells that regenerate the missing tissue. We have identified the expression of von Willebrand Factor D and EGF Domains (vwde) as a common feature of blastemas capable of regenerating limbs and fins in a variety of highly regenerative species. Further, vwde expression is tightly linked to the ability to regenerate appendages. Functional experiments demonstrate a requirement for vwde in regeneration and indicate that Vwde is a potent mitogen in the blastema. These data identify a key role for vwde in regenerating blastemas and underscore the power of an evolutionarily-informed approach for identifying conserved genetic components of regeneration.

developmental biology↗

bioRxiv2018

Deep evolutionary origin of limb and fin regeneration

Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of complete limb and paired fin regeneration, respectively. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in Polypterid fishes (Cladistia). Whether complete appendage regeneration in sarcopterygians and actinopterygians evolved independently or has a common origin remains unknown. Here we combine fin regeneration assays and comparative RNA-seq analysis to provide support for a common origin of a paired appendage regeneration in osteichthyes (bony vertebrates). We show that, in addition to Polypterids, regeneration after fin endoskeleton amputation occurs in extant representatives of all major actinopterygian clades: the American paddlefish, (Chondrostei), the spotted gar (Holostei), as well as in two cichlid species, the white convict and the oscar (Teleostei). Our comparative RNA-seq analysis of regenerating blastemas of axolotl and Polypterus reveals the activation of common genetic pathways and expression profiles, consistent with a pan-osteichthyes genetic program of appendage regeneration. Collectively, our findings support a deep evolutionary origin of paired appendage regeneration in osteichthyes and provide an evolutionary framework for studies on the genetic basis of appendage regeneration.

evolutionary biology↗

bioRxiv2018

A dual function of FGF signaling in Xenopus left-right axis formation

Organ left-right (LR) asymmetry is a conserved vertebrate feature, which is regulated by left-sided activation of Nodal signaling. Nodal asymmetry is established by a leftward fluid-flow generated at the ciliated LR organizer (LRO). While the role of fibroblast growth factor (FGF) signaling pathways during mesoderm development are conserved, diverging results from different model organisms suggested a non-conserved function in LR asymmetry. Here, we demonstrate that FGF is required during gastrulation in a dual function at consecutive stages of Xenopus embryonic development. In the early gastrula, FGF is necessary for LRO precursor induction, acting in parallel to FGF-mediated mesoderm induction. During late gastrulation, the FGF/Ca2+-branch is required for specification of the flow sensing lateral LRO cells, a function related to FGF-mediated mesoderm morphogenesis. This second function in addition requires input from the calcium channel Polycystin-2. Thus, analogous to mesoderm development, FGF activity is required in a dual role for laterality specification, namely for generating and sensing of leftward flow. Moreover, our data show that FGF functions in LR asymmetric development are conserved across vertebrate species, from fish to mammals.

developmental biology↗

bioRxiv2017

Disruption of dual zygotic spindle assembly shows epigenetic asymmetry to be chromosome intrinsic

At the beginning of mammalian life the genetic material from each parent meets when the fertilized egg divides. It was previously thought that a single microtubule spindle is responsible to spatially combine the two genomes and then segregate them to create the two-cell embryo. Utilizing light-sheet microscopy, we showed that two bipolar spindles form in the zygote, that independently congress the maternal and paternal genomes. These two spindles aligned their poles prior to anaphase but kept the parental genomes apart during the first cleavage. This spindle assembly mechanism provides a rationale for erroneous divisions into more than two blastomeric nuclei observed in mammalian zygotes and reveals the mechanism behind the observation that parental genomes occupy separate nuclear compartments in the two-cell embryo.\n\nOne Sentence Summary: After fertilization, two spindles form around pro-nuclei in mammalian zygotes and keep the parental genomes apart during the first division.

cell biology↗