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Results for “Developmental Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 865 records · Page 48Linked to original sources

bioRxiv2020

MicroRNA-24-3p promotes skeletal muscle differentiation and regeneration by regulating high mobility group AT-hook 1

Numerous studies have established the critical roles of microRNAs in regulating post-transcriptional gene expression in diverse biological processes. Here, we report on the role and mechanism of miR-24-3p in skeletal muscle differentiation and regeneration. miR-24-3p promotes myoblast differentiation and skeletal muscle regeneration by directly targeting high mobility group AT-hook 1 (HMGA1) and regulating it and its direct downstream target, the inhibitor of differentiation 3 (ID3). miR-24-3p knockdown in neonatal mice increases PAX7-positive proliferating muscle stem cells (MuSCs) by derepressing Hmga1 and Id3. Similarly, inhibition of miR-24-3p in the tibialis anterior muscle prevents Hmga1 and Id3 downregulation and impairs regeneration. These findings provide evidence that the miR-24-3p/HMGA1/ID3 axis is required for MuSC differentiation and skeletal muscle regeneration in vivo.

developmental biology↗

bioRxiv2023

SIN-3 transcriptional coregulator maintains mitochondrial hormesis and polyamine flux

Mitochondrial function relies on the coordinated transcription of mitochondrial and nuclear genomes to assemble respiratory chain complexes. Across species, the SIN3 coregulator influences mitochondrial functions, but how its loss impacts mitochondrial homeostasis and metabolism in the context of a whole organism is unknown. Exploring this link is important because SIN3 haploinsufficiency causes intellectual disability/autism syndromes and SIN3 plays an important role in tumor biology. Here we show that loss of C. elegans SIN-3 results in transcriptional deregulation of mitochondrial- and nuclear encoded mitochondrial genes, potentially leading to mito-nuclear imbalance. Consistent with impaired mitochondrial function, sin-3 mutants show extensive mitochondrial fragmentation by transmission electron microscopy (TEM) and in vivo imaging, and altered oxygen consumption. Metabolomic analysis of sin-3 mutant animals identifies a signature of mitochondria stress, and deregulation of methionine flux resulting in decreased S-adenosyl methionine (SAM), and increased polyamine levels. Our results identify SIN3 as a key regulator of mitochondrial dynamics and metabolic flux, with important implications for human pathologies.

developmental biology↗

bioRxiv2018

Mettl14 is required for mouse post-implantation development by facilitating epiblast maturation

N6-methyladenosine (m6A) is the most prevalent and reversible internal modification of mammalian messenger and noncoding RNAs mediated by specific m6A writer, reader, and eraser proteins. As an m6A writer, the METTL3-METTL14-WTAP complex dynamically regulates m6A modification and plays important roles in diverse biological processes. However, our knowledge about the complete functions of this RNA methyltransferase complex, the contributions of each component to the methylation and their impacts on different biological pathways, are still very limited. Here, by employing both in vivo and in vitro models, we report that METTL14 was indispensable for post-implantation embryonic development by facilitating the conversion from naive to primed state of the epiblast. Depletion of Mettl14 lead to conspicuous embryonic growth retardation from E6.5 mainly as a result of resistance to differentiation, which further lead to embryonic lethality early in gestation. Our data highlight the critical function of METTL14, as an m6A modification regulator, in orchestrating early mouse embryogenesis.

developmental biology↗

bioRxiv2022

Molecular characterization of cell types in the squid Loligo vulgaris

Cephalopods have long been getting a lot of attention for their fascinating behavioral abilities and for the complexity of their nervous systems that set them apart from other mollusks. Because of the great evolutionary distance that separates vertebrates from mollusks, it is evident that higher cognitive features have evolved independently in this clade although they sometimes resemble cognitive functions of vertebrates. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Gaining a better understanding of the biology of various species of cephalopods can significantly improve our knowledge of how these animals evolved and better identify the mechanisms that drive the astonishing faculties of their nervous systems. In this study, we performed single-cell transcriptomics of whole heads of Loligo vulgaris pre-hatchlings. We characterized the different cell types in the head of these animals and explored the expression patterns of core cell type markers by hybridization chain reaction. We were able to thoroughly describe some major components of the squid nervous that play important roles for the maintenance, development and sensory function in the nervous system of these animals.

developmental biology↗

bioRxiv2023

TOBF1 modulates mouse embryonic stem cell fate through co-transcriptional regulation of alternative splicing

Embryonic stem (ES) cells retain the ability to undergo lineage-specific differentiation that can eventually give rise to different cell types that constitute an organism. Although stem cell specific biological networks of transcription factors and epigenetic modifiers are well established, how the ES cell specific transcriptional and alternative splicing (AS) machinery regulate their expression has not been sufficiently explored. In this study, we show that the lncRNA associated protein TOBF1 regulates the co-transcriptional alternative splicing of transcripts necessary for maintaining stem cell identity in mouse ES cells. Overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and alternative splicing upon its disruption unmasked local nuclear territories where these distinct events converge, ultimately leading to the maintenance of mouse ES cell identity.

developmental biology↗

bioRxiv2025

Single-Nucleotide m6A Mapping Uncovers Redundant YTHDF Function in Planarian Progenitor Fate Selection

Cell fate decisions require tight regulation of gene expression. In planarians--highly regenerative flatworms--the mRNA modification N6-methyladenosine (m6A) modulates progenitor production and fate. However, the mechanisms governing m6A deposition in the planarian transcriptome--and the role of their expanded family of YTHDF m6A reader proteins in orchestrating biological functions--remain unclear. Here, we generated the first single-nucleotide resolution map of m6A in planarians, and revealed that simple sequence rules guide m6A deposition, facilitating the flexible evolutionary gain and loss of these marks. Functional analyses of the five planarian m6A readers revealed that while individual reader expression is dispensable, together, the planarian readers regulate the production of specific progenitor lineages and overall body size. Collectively, our findings uncover a robust, redundant regulatory architecture, characterized by multiple m6A sites per gene and coordinated m6A reader expression. This architecture is essential for proper lineage resolution and provides insights into the evolutionary dynamics of the m6A landscape.

developmental biology↗

bioRxiv2018

The long noncoding RNA Hand2as orchestrates heart development through regulation of precise expression of HAND2

Rigorous exploration and dissection of potential actions and effects of long noncoding RNA (lncRNA) in animals remain challenging. Here using multiple knockout mouse models and single-cell RNA sequencing, we demonstrate that the divergent lncRNA Hand2as has a key, complex modulatory effect on the expression of its neighboring gene HAND2 and subsequently on heart development and function, largely independent of Hand2as transcription and transcripts. Full-length deletion of Hand2as in mouse causes moderate yet prevalent upregulation of HAND2 in hundreds of cardiac cells, resulting in profound biological consequences, including dysregulated cardiac gene programs, congenital heart defects and perinatal lethality. We propose a cis-functional role for the Hand2as locus in dampening HAND2 expression to restrain cardiomyocyte proliferation, thereby orchestrating a balanced development of cardiac cell lineages. This study highlights the need for complementary genetic and single-cell approaches to delineate the function and primary molecular effects of an lncRNA in animals.\n\nImpact statementThe long noncoding RNA Hand2as critically controls the precise expression of its neighboring gene HAND2, thereby balancing cardiac lineages and expression programs that are essential for heart development and function.

developmental biology↗

bioRxiv2025

Progressive mural cell deficiencies across the lifespan in a foxf2 model of Cerebral Small Vessel Disease

Cerebral Small Vessel Disease (SVD) is a leading cause of stroke and dementia and yet is often an incidental finding in aged patients due to the inaccessibility of brain vasculature to imaging. Animal models are important for modelling the development and progression of SVD across the lifespan. In humans, reduced FOXF2 is associated with an increased stroke risk and SVD prevalence in humans. In the zebrafish, foxf2 is expressed in pericytes and vascular smooth muscle cells and is involved in vascular stability. We use partial foxf2 loss of function (foxf2a-/-) to model the lifespan effect of reduced Foxf2 on small vessel biology. We find that the initial pool of pericytes in developing foxf2a mutants is strongly reduced. The few brain pericytes present in mutants have strikingly longer processes and enlarged soma. foxf2a mutant pericytes can partially repopulate the brain after ablation suggesting some recovery is possible. Despite this capacity, adult foxf2a mutant brains show regional heterogeneity, with some areas of normality and others with severe pericyte depletion. Taken together, foxf2a mutants fail to generate a sufficient initial population of pericytes. The pericytes that remain have abnormal cell morphology. Over the lifespan, initial pericyte deficits are not repaired and lead to severely abnormal cerebrovasculature in adults. This work opens new avenues for modeling progressive genetic forms of human Cerebral Small Vessel Disease.

developmental biology↗

bioRxiv2019

Endocardial differentiation in zebrafish occurs during early somitogenesis and is dependent on BMP and etv2 signalling

Abstract The endocardium and adjacent vascular endothelial network share a number of molecular markers however there are distinct physiological functions of these tissues. What distinguishes these lineages on a molecular level remains an important, unanswered question in cardiovascular biology. We have identified the Gt(SAGFF27C); Tg(4xUAS:egfp) line as a marker of early endocardial development and used this line to examine endocardial differentiation. Our results show that the endocardium emerges from the anterior lateral plate mesoderm at the 8-somite stage (13 hpf). Analysis in a number of loss-of-function models showed that whilst nkx2.5, hand2 and tal1 loss-of-function have no effect on the endocardial progenitor domain, both etv2 loss-of-function and inhibition of BMP signalling reduce the endocardial domain. Furthermore, manipulating BMP signalling alters etv2 expression. Together, these results describe the onset of endocardial molecular identity and suggest a signalling cascade whereby BMP signalling acts upstream of etv2 to direct differentiation of endocardial progenitors.

developmental biology↗

bioRxiv2023

Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells

Highly potent animal stem cells either self renew or launch complex differentiation programs, using mechanisms that are only partly understood. Drosophila female germline stem cells (GSC) perpetuate without change over evolutionary time and generate cystoblast daughters that develop into nurse cells and oocytes. Cystoblasts initiate differentiation by generating a transient syncytial state, the germline cyst, and by increasing pericentromeric H3K9me3 modification, actions likely to suppress transposable element activity. Relatively open GSC chromatin is further restricted by Polycomb repression of testis or somatic cell-expressed genes briefly active in early female germ cells. Subsequently, Neijre/CBP and Myc help upregulate growth and reprogram GSC metabolism by altering mitochondrial transmembrane transport, gluconeogenesis and other processes. In all these respects GSC differentiation resembles development of the totipotent zygote. We propose that the totipotent stem cell state was shaped by the need to resist transposon activity over evolutionary time scales.

developmental biology↗

bioRxiv2021

Proapoptotic RHG genes and mitochondria play a key non-apoptotic role in remodelling the Drosophila sensory system

Caspases are best known for their role in programmed cell death but have also been found to be important in several non-apoptotic phenomena such as cell fate specification, cell migration and terminal differentiation. The dynamics of such sub-lethal caspase events and the molecular mechanisms regulating them are still largely unknown. As more tools for visualizing and manipulating caspase activation in vivo become available, greater insights into this biology are being made. Using a new and sensitive in vivo effector caspase probe, called SR4VH, we demonstrate that effector caspases are activated in pruning sensory neurons earlier than previously thought and that the level of caspase activation in these neurons is consistently lower than in neurons undergoing cell death. We reveal that Grim and Reaper, two of the four pro-apoptotic RHG proteins, are required for sensory neuron pruning and that disrupting the dynamics of the mitochondrial network prevents effector caspase activation in both pruning and dying sensory neurons. Overall, our findings demonstrate that a sublethal deployment of the apoptotic machinery is critical for remodelling dendrites and also reveal a direct link between mitochondria and sensory neuron cell death in vivo.

developmental biology↗

bioRxiv2025

Protein kinase C inhibitor suppresses 2-cell stage development and perinuclear vesicle formation in mouse zygotes

Nuclear structure and nucleocytoplasmic interaction are closely linked to the regulation of cellular and higher-order biological processes. An alternative pathway for nucleocytoplasmic transport involving perinuclear vesicle formation and release, termed nuclear envelope budding (NEB), has been observed in diverse species and cell types. NEB-like events have also been reported in mammalian zygotes, including mice. However, their molecular basis remains unclear. Recent results suggest that protein kinase C (PKC) signaling regulates perinuclear vesicle biogenesis during NEB. While multiple PKC isoforms are expressed in mouse oocytes, their functions in zygotes are not fully understood. We investigated the effects of pharmacological PKC inhibition on zygotic development and NEB-like perinuclear vesicle formation. Our results suggest that NEB-like events in mouse zygotes may involve PKC-dependent mechanisms and that PKC activity might be critical for the 1-to 2-cell transition.

developmental biology↗

bioRxiv2021

Tig1 regulates proximo-distal identity during salamander limb regeneration

Salamander limb regeneration is an accurate process which gives rise exclusively to the missing structures, irrespective of the amputation level. This suggests that cells in the stump have an awareness of their spatial location, a property termed positional identity. Little is known about how positional identity is encoded, in salamanders or other biological systems. Through single-cell RNAseq analysis, we identified Tig1/Rarres1 as a potential determinant of proximal identity. Tig1 encodes a conserved cell surface molecule, is regulated by retinoic acid and exhibits a graded expression along the proximo-distal axis of the limb. Its overexpression leads to regeneration defects in the distal elements and elicits proximal displacement of blastema cells, while its neutralisation blocks proximo-distal cell surface interactions. Critically, Tig1 reprogrammes distal cells to a proximal identity, upregulating Prod1 and inhibiting Hoxa13 and distal transcriptional networks. Thus, Tig1 is a central cell surface determinant of proximal identity in the salamander limb.

developmental biology↗

bioRxiv2022

Tiling mechanisms of the compound eye through geometrical tessellation

Tilling patterns are observed in many biological structures. Hexagonal tilling, commonly observed in the compound eyes of wild-type Drosophila, is dominant in nature; this dominance can probably be attributed to physical restrictions such as structural robustness, minimal boundary length, and space filling efficiency. Surprisingly, tetragonal tiling patterns are also observed in some Drosophila small eye mutants and aquatic crustaceans. Herein, geometrical tessellation is shown to determine the ommatidial tiling patterns. In small eye mutants, the hexagonal pattern is transformed into a tetragonal pattern as the relative positions of neighboring ommatidia are stretched along the dorsal-ventral axis. Hence, the regular distribution of ommatidia and their uniform growth collectively play an essential role in the establishment of tetragonal and hexagonal tiling patterns in compound eyes.

developmental biology↗

bioRxiv2025

Human genetic studies and zebrafish models identify Plxna4 as a regulator of adiposity, somatic growth, and feeding behaviours

Obesity is a major public health crisis, affecting billions worldwide and increasing the risk of metabolic and cardiovascular diseases. While lifestyle factors play a role, genetic variation is a key determinant of both obesity susceptibility and the efficacy of treatment strategies. Recent studies have implicated the Semaphorin 3 signalling pathway in obesity; however, specific roles for pathway components remain largely unexplored. Here, we focus on Class A Plexins and their potential contributions to body weight regulation. Using large-scale genetic association data, we identified that rare, predicted loss-of-function mutations in PLXNA4 were associated with body mass index (BMI) in females. Furthermore, common variant analysis revealed that genetic variation at PLXNA4 was linked to BMI, height, and various neuropsychiatric disorders. To investigate the biological role of Plxna4, we generated zebrafish plxna4 loss-of-function mutants, which exhibited an 85-92% reduction in Plxna4 protein. Despite appearing morphologically normal, mutant zebrafish at juvenile stages were shorter, had increased body fat levels relative to size-matched wild-type siblings, and displayed hypertrophic subcutaneous adipose tissue. Feeding assays revealed that plxna4 mutants consumed more food than wild-type siblings and exhibited food-stimulated hyperactivity, characterised by increased swimming speed, higher speed variability, and frequent high-speed bursts. Together, these findings demonstrate a conserved role for Plxna4 in regulating feeding behaviour and body fat levels, providing new insights into the genetic basis of obesity and warranting further studies to elucidate the molecular mechanisms underlying these effects.

developmental biology↗

bioRxiv2020

Segmentation of the Zebrafish Brain Vasculature from Light Sheet Fluorescence Microscopy Datasets

Light sheet fluorescent microscopy allows imaging of zebrafish vascular development in great detail. However, interpretation of data often relies on visual assessment and approaches to validate image analysis steps are broadly lacking. Here, we compare different enhancement and segmentation approaches to extract the zebrafish cerebral vasculature, provide comprehensive validation, study segmentation robustness, examine sensitivity, apply the validated method to quantify embryonic cerebrovascular volume, and examine applicability to different transgenic reporter lines. The best performing segmentation method was used to train different deep learning networks for segmentation. We found that U-Net based architectures outperform SegNet. While there was a slight overestimation of vascular volume using the U-Net methodologies, variances were low, suggesting that sensitivity to biological changes would still be obtained. HighlightsO_LIGeneral filtering is less applicable than Sato enhancement to enhance zebrafish cerebral vessels. C_LIO_LIBiological data sets help to overcome the lack of segmentation gold-standards and phantom models. C_LIO_LISato enhancement followed by Otsu thresholding is highly accurate, robust, and sensitive. C_LIO_LIDirect generalization of the segmentation approach to transgenics, other than the one optimized for, should be treated with caution. C_LIO_LIDeep learning based segmentation is applicable to the zebrafish cerebral vasculature, with U-Net based architectures outperforming SegNet architectures. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/213843v1_ufig1.gif" ALT="Figure 1"> View larger version (88K): org.highwire.dtl.DTLVardef@6b45a3org.highwire.dtl.DTLVardef@a90c0borg.highwire.dtl.DTLVardef@55be1borg.highwire.dtl.DTLVardef@1340df9_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2024

Identifying the molecular basis for functional divergence of duplicated SOX factors controlling endoderm formation and left-right patterning in zebrafish

Endoderm, one of three primary germ layers of vertebrate embryos, makes major contributions to the respiratory and gastrointestinal tracts and associated organs, including liver and pancreas. In mammals, the transcription factor SOX17 is vital for endoderm organ formation and can induce endoderm progenitor identity. Duplication of ancestral sox17 in the teleost lineage produced the paralogues sox32 and sox17 in zebrafish. Sox32 is required for specification of endoderm and progenitors of the left-right organiser (Kupffers Vesicle, KV), with Sox17 a downstream target of Sox32 that is implicated in further KV development. Phenotypic evidence therefore suggests functional similarities between zebrafish Sox32 and Sox17 and mammalian SOX17. Here, we directly compare these orthologues and paralogues, using the early zebrafish embryo as a biological platform for functional testing. Our results indicate that, unlike Sox32, human SOX17 cannot induce endoderm specification in zebrafish. Furthermore, using hybrid protein functional analyses, we show that Sox32 specificity for the endoderm gene regulatory network is linked to evolutionary divergence in its DNA-binding HMG domain from its paralogue Sox17. Additionally, changes in the C-terminal regions of Sox32 and Sox17 underpin their differing target specificities. Finally, we establish that specific conserved peptides in the C-terminal domain are essential for the role of Sox17 in establishing correct organ asymmetry. Overall, our results illuminate the molecular basis for functional divergence of Sox32 and Sox17 in vertebrate endoderm development and left-right patterning, and the evolution of SoxF transcription factor function.

developmental biology↗

bioRxiv2021

Epigenetic models predict age and aging in plains zebras and other equids

Five of the seven extant wild species of the genus Equus are species of significant conservation concern. Effective conservation and management of such threatened wildlife populations depends on the ability to estimate demographic trends and population viability and therefore requires accurate assessment of age structure. However, reliably aging wildlife is challenging as many methods are highly invasive, inaccurate, or both. Epigenetic aging models, which estimate individual age with high accuracy based on genomic methylation patterns, are promising developments in this regard. Importantly, epigenetic aging models developed for one species can potentially predict age with high accuracy in sister taxa. Using blood and biopsy samples from known age plains zebras (Equus quagga), we developed epigenetic clocks (ECs) to predict chronological age, and epigenetic pacemaker (EPM) models to predict biological age. We tested the ability of our blood-based EC to predict ages of Grevys zebras, Somali asses and domestic horses, from blood samples. Because our samples came from a population with a complex pedigree, we also leveraged information from a previous sequencing effort to measure the association between levels of inbreeding (F and ROH) and the age acceleration as measured by DNA methylation. The resulting models describe the trajectory of epigenetic aging in plains zebras and accurately predict the ages of plains zebras and other equids. We found moderate support for a slight acceleration of aging with increased inbreeding.

developmental biology↗