Biology subjects

Leyhr, J.

Publications and source records attributed to Leyhr, J..

7 recordsLinked to original sources

bioRxiv2026

Reconstruction of the Prox gene family evolution in vertebrates reveals multiple lineage-specific gene losses

Prospero-related homeobox (Prox) genes encode a family of transcription factors that play essential roles in the development of several organs and systems, including the central nervous system, lymphatic endothelium, musculature, and liver. Despite their developmental importance, the evolutionary history of the vertebrate Prox gene family remains poorly understood. In this study we combined phylogenetic and synteny analysis to characterise the evolution of the Prox family in vertebrates. Our results reveal that two to three Prox subfamilies were already present in the last common ancestor of jawed vertebrates. We clarify the identity and evolutionary relationships of well-studied members of this family and identify multiple independent losses of Prox2 and Prox3 genes in specific vertebrate lineages. Furthermore, we uncover evidence for the existence of a fourth Prox gene in the ancestral vertebrate genome, which was subsequently lost. Overall, this study provides the first comprehensive analysis of the evolutionary history of the vertebrate Prox gene family and establishes a foundations for future studies on the functional roles of these genes.

genomics↗

bioRxiv2025

WormTagDB: A Systematic Survey of Endogenously Tagged Proteins in C. elegans and Roadmap Towards the Tagged Proteome

Endogenous protein tagging in Caenorhabditis elegans enables direct visualization and manipulation of proteins in vivo, providing native readouts of expression, localization, and dynamics. No coordinated effort currently exists to comprehensively tag proteins on a large scale, resulting in patchy coverage that limits comprehensive proteome analyses. We systematically reviewed 2,500 primary research articles, identifying 778 that report novel endogenous tags, and integrated these with the Caenorhabditis Genetics Center strain records to catalog >90% of all existing tagged alleles. In total, we found that 1,554 unique genes (~8% of the proteome) have been endogenously tagged. Gene Ontology enrichment analysis revealed that cytoskeletal proteins, transcription factors, and RNA-binding proteins dominate the tagged proteome, while membrane proteins, metabolic enzymes, and mitochondrial components remain largely untagged, reflecting both technical barriers and research priorities that have shaped the last decade of tagging efforts. We created WormTagDB (https://wormtagdb.rc.duke.edu), an interactive, community-updatable resource that consolidates all known endogenously tagged alleles and provides precomputed CRISPR guide and homology-arm primer designs for N- and C-terminal knock-ins across all protein-coding genes. This will enable researchers to easily identify existing alleles to prevent redundant strain generation and rapidly initiate new knock-in experiments. A systematic effort to tag every C. elegans gene would deliver the first complete metazoan visual proteome, providing comprehensive insights into protein localization, dynamics, and regulation, revealing new protein associations and molecular processes.

genetics↗

bioRxiv2024

The sensory shark: high-quality phenotypic, genomic and transcriptomic data for the small spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates

Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterise general aspects of the catshark genome, confirming the high conservation of genome organisation across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electro-sensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the Transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.

evolutionary biology↗

bioRxiv2023

The overlooked first intercostal ligament: Does it help to stabilize the Weberian apparatus?

The Weberian apparatus is a novel hearing adaptation that facilitates increased hearing sensitivity in otophysan fishes. The apparatus is a complex system composed of modifications to anterior vertebral elements, the inner ear, and the swim bladder. A critical piece of the system that often receives minor attention are the various ligaments that bridge these three regions. Most famous of the ligaments is the interossicular ligament, which connects the weberian ossicle chain (scaphium-intercalarium-tripus). Several other ligaments are present, including the suspensor (tripus to parapophysis 4) and the triple ligament (tripus-os suspensorium-tunica externa). Here, by combining diffusible iodine-based contrast enhancement (DICE) and propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SRCT) with classic histological methods we shine new light on the first intercostal ligament (ICL1) and discuss its potential function in relation to the Weberian apparatus. ICL1 is nearly absent from the cypriniform literature, typically only mentioned in a general discussion together with other intercostal ligaments. This study examines the development and structure of ICL1 comparatively with the other definitive Weberian ligaments in the zebrafish (Danio rerio). We provide a comprehensive view of development, three-dimensional shape, and composition to generate hypotheses regarding potential functions of ICL1 within the greater Weberian apparatus. Given new detail presented herein regarding the structure of ICL1, modifications to rib 5 and parapophysis 4 for ICL1 attachment, and the alignment of ICL1 with the os suspensorium, we propose a supportive (anchoring) role of ICL1 to aid in minimizing non-optimal movement of the structures of the fourth vertebra, thereby allowing the focus of vibrations anteriorly to the ossicle chain with minimal signal loss in zebrafish and other species with similar Weberian apparatus morphologies. We conclude that ICL1 should be included in future analyses of Weberian apparatus function where ligaments are addressed.

developmental biology↗

bioRxiv2021

An evolutionarily conserved cis-regulatory element of Nkx3.2 contributes to early jaw joint morphology in zebrafish

The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in gnathostomes but undetectable in the jawless hagfish. This enhancer is active in the developing jaw joint region of the zebrafish Danio rerio, and was thus designated as jaw joint regulatory sequence 1 (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 leads to a transient jaw joint deformation and partial fusion. Emergence of this Nkx3.2 enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.

developmental biology↗

bioRxiv2021

The role of Gdf5 in the development of the zebrafish fin endoskeleton

BackgroundThe development of the vertebrate limb skeleton requires a complex interaction of multiple factors to facilitate correct shaping and positioning of bones and joints. Growth and differentiation factor 5 (Gdf5), a member of the transforming growth factor-beta family (TGF-{beta}) is involved in patterning appendicular skeletal elements including joints. Expression of gdf5 in zebrafish has been detected within the first pharyngeal arch jaw joint, fin mesenchyme condensations and segmentation zones in median fins, however little is known about the functional role of Gdf5 outside of Amniota. ResultsWe generated CRISPR/Cas9 knockout of gdf5 in zebrafish and analysed the resulting phenotype at different developmental stages. Homozygous gdf5 mutant zebrafish displayed changes in segmentation of the endoskeletal disc and, in consequence, loss of posterior radials in the pectoral fins. Mutant fish also displayed affected organisation and length of skeletal elements in the median fins, however joint formation and mineralisation process seemed unaffected. ConclusionsOur study demonstrates the importance of Gdf5 for the paired and median fin endoskeleton development in zebrafish and reveals that the severity of the effect increases from anterior to posterior side of the elements. Our findings are consistent with phenotypes observed in human and mouse appendicular skeleton in response to Gdf5 knockout, suggesting a broadly conserved role for Gdf5 in Osteichthyes.

developmental biology↗

bioRxiv2020

The Broad Role of Nkx3.2 in the Development of the Zebrafish Axial Skeleton

The transcription factor Nkx3.2 (Bapx1) is an important chondrocyte maturation inhibitor. Previous Nkx3.2 knock-down and overexpression studies in non-mammalian gnathostomes have focused on its role in primary jaw joint development, while little is known about the function of this gene in broader skeletal development. We generated CRISPR/Cas9 knockout of nkx3.2 in zebrafish and applied a range of techniques to characterize skeletal phenotypes at developmental stages from larva to adult, revealing fusions in bones of the occiput, the loss or deformation of bony elements derived from basiventral cartilages of the vertebrae, and an increased length of the proximal radials of the dorsal and anal fins. These phenotypes are reminiscent of Nkx3.2 knockout phenotypes in mammals, suggesting that the function of this gene in axial skeletal development is ancestral to osteichthyans. Our results highlight the broad role of nkx3.2 in zebrafish skeletal development and its context-specific functions in different skeletal elements.

developmental biology↗