Biology subjects

Williams, M. K.

Publications and source records attributed to Williams, M. K..

5 recordsLinked to original sources

bioRxiv2025

Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish

Gene expression changes across embryonic development reflect both differentiation and genes whose expression varies strictly with developmental time, independent of cell type. Multiple embryonic timing systems set the onset and pace of developmental events, and blocking transcription arrests many of these events. However, the genes comprising the vertebrate embryonic timing system(s) remain largely unknown. To identify genes whose expression changes with time alone, we examine naive zebrafish embryonic explants that form only two tissue types yet maintain developmental timing, thus uncoupling developmental age from most differentiation programs. By comparing longitudinal gene expression in naive explants with Nodal-induced explants that differentiate into all three germ layers, we identify "timekeeping" genes whose temporal expression patterns vary strictly with developmental age. Consensus clustering of temporally dynamic genes identified 20 gene clusters, termed "chrono-constitutive modules" (CCMs), that maintain distinct schedules of expression regardless of tissue type. These CCM trajectories are similar in intact zebrafish embryos and single embryonic cells of multiple distinct lineages. Enrichment analysis of microRNA targets and transcription factor regulons within the CCMs further reveal distinct putative regulators of several modules. Strikingly, CCM expression patterns are also largely conserved during early development of another fish species, Japanese medaka. Machine learning models trained on only zebrafish CCM transcript levels accurately predict the developmental age of embryonic explants, intact embryos, and even individual embryonic cells, demonstrating their utility in developmental timekeeping. These results support the existence of transcriptional timekeeping during early development and demonstrate its utility in embryonic stage prediction.

developmental biology↗

bioRxiv2025

Dorsal forerunner cells transmit epiboly forces to extend the zebrafish notochord

Convergence and extension (C&E) cell movements promote anteroposterior axis extension and narrow both neuroectodermal and mesodermal tissues during gastrulation. Mediolateral cell intercalation is largely responsible for this morphogenetic process in vertebrates, but evidence suggests that additional cell-extrinsic forces generated by surrounding tissues contribute to the shaping of many structures. In zebrafish, for example, mechanical forces generated by the anteriorly migrating prechordal plate cooperate with tissue-autonomous cell intercalations to promote extension of the notochord. Here we propose a novel model for notochord morphogenesis by which mechanical epiboly forces within the enveloping layer are transmitted to the posterior end of the notochord via a cluster of dorsal forerunner cells (DFCs) that physically links the two. We found that scattering or absence of DFCs caused by loss of crb2a or sox32, respectively, reduces notochord C&E and exacerbates axis extension defects in planar cell polarity signaling-deficient embryos. Using an automated image segmentation and cell shape analysis pipeline, we show that cells within the posterior notochord fail to properly elongate when DFCs are scattered or absent. Finally, we demonstrate that loss of crb2a and sox32 fails to disrupt C&E of zebrafish embryonic explants in which no epiboly occurs and all extension is driven by cell-intrinsic behaviors. Together, these findings support a model in which DFCs facilitate mechanical coupling of the enveloping layer to the posterior notochord during epiboly to ensure its robust morphogenesis during gastrulation.

developmental biology↗

bioRxiv2025

Sulfatase modifying factors control the timing of zebrafish gastrulation morphogenesis

To shape the emerging body plan, morphogenetic cell movements must be coordinated not only in space, but also in time. Convergence and Extension (C&E) movements that elongate the anteroposterior axis initiate with precise timing during vertebrate gastrulation, but the mechanisms controlling their onset remain unknown. We examined this question using zebrafish embryonic explants that faithfully recapitulate C&E cell movements and their precise timing in culture, in isolation from other gastrulation movements. We determined that new transcription is required at gastrulation onset for C&E in explants and identified sulfatase modifying factor 2 (sumf2) as a candidate trigger gene expressed at this time. sumf2 and its paralog sumf1 encode negative and positive regulators, respectively, of all sulfatase enzymes, which remove sulfate groups from their substrates, altering their biological activity. In zebrafish embryos and explants, sumf1 and sumf2 expression levels invert at gastrulation onset, predicting a reduction in sulfatase activity and consequent increase of substrate sulfation. We found that overexpressing sumf1 and sumf2 causes delayed or precocious C&E onset, respectively, whereas loss of sumf1 and sumf2 function shifts C&E timing in the opposite direction. We further identified Sulf1, an extracellular sulfatase that modifies heparan sulfate proteoglycans (HSPGs), as the key effector by which sumf1 and sumf2 control C&E timing. Accordingly, reduced or increased levels of sulfated heparan sulfate similarly shift C&E onset and suppress sumf1 and sumf2 mutant phenotypes. Together, our work supports a model in which sumf2 expression at zebrafish gastrulation onset reduces sulfatase activity, rewriting HSPG sulfation patterns to promote and/or permit C&E morphogenesis.

developmental biology↗

bioRxiv2024

Temporal dynamics of BMP/Nodal ratio drive tissue-specific gastrulation morphogenesis

Anteroposterior (AP) elongation of the vertebrate body plan is driven by convergence and extension (C&E) gastrulation movements in both the mesoderm and neuroectoderm, but how or whether molecular regulation of C&E differs between tissues remains an open question. Using a zebrafish explant model of AP axis extension, we show that C&E of the neuroectoderm and mesoderm can be uncoupled ex vivo, and that morphogenesis of individual tissues results from distinct morphogen signaling dynamics. Using precise temporal manipulation of BMP and Nodal signaling, we identify a critical developmental window during which high or low BMP/Nodal ratios induce neuroectoderm- or mesoderm-driven C&E, respectively. Increased BMP activity similarly enhances C&E specifically in the ectoderm of intact zebrafish gastrulae, highlighting the in vivo relevance of our findings. Together, these results demonstrate that temporal dynamics of BMP and Nodal morphogen signaling activate distinct morphogenetic programs governing C&E gastrulation movements within individual tissues. SUMMARY STATEMENTUsing zebrafish embryo and explant models, we demonstrate that temporal dynamics of morphogen signaling ratios distinguish between tissue-specific morphogenetic programs during vertebrate body plan formation.

developmental biology↗

bioRxiv2023

Vangl2 deficient zebrafish exhibit hallmarks of neural tube closure defects

Shaping of the future brain and spinal cord during neurulation is an essential component of early vertebrate development. In amniote embryos, primary neurulation occurs through a "fold-and-fuse" mechanism by which the edges of the neural plate fuse into the hollow neural tube. Failure of neural fold fusion results in neural tube defects (NTDs), which are among the most devastating and common congenital anomalies worldwide. Unlike amniotes, the zebrafish neural tube develops largely via formation of a solid neural keel that later cavitates to form a midline lumen. Although many aspects of primary neurulation are conserved in zebrafish, including neural fold zippering, it was not clear how well these events resemble analogous processes in amniote embryos. Here, we demonstrate that despite outward differences, zebrafish anterior neurulation closely resembles that of mammals. For the first time in zebrafish embryos, we directly observe enclosure of a lumen by the bilateral neural folds, which fuse by zippering between at least two distinct closure sites. Both the apical constriction that elevates the neural folds and the zippering that fuses them coincide with apical Myosin enrichment. We further show that embryos lacking vangl2, a core planar cell polarity and NTD risk gene, exhibit delayed and abnormal neural fold fusion that fails to enclose a lumen. These defects can also be observed in fixed embryos, enabling their detection without live imaging. Together, our data provide direct evidence for fold-and-fuse neurulation in zebrafish and its disruption upon loss of an NTD risk gene, highlighting the deep conservation of primary neurulation across vertebrates. HighlightsO_LIThe anterior neural tube of zebrafish undergoes "fold-and-fuse" neurulation to enclose a lumen, highlighting conservation of primary neurulation mechanisms across vertebrates. C_LIO_LIAnterior neural tube closure is delayed and abnormal in zebrafish embryos lacking the planar cell polarity gene vangl2, occurring by excessive "buttoning" rather than smooth "zippering" and failing to enclose a lumen. C_LIO_LINeural tube defects (NTDs) are visible in fixed vangl2 deficient embryos, enabling simple assessment of neural tube phenotypes with potential utility in screening NTD risk genes. C_LI

developmental biology↗