SEARCH · Search bioRxiv

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 649 records · Page 36Linked to original sources

bioRxiv2018

Blimp-1 mediates the temporal control of embryonic tube maturation

The specification of tissue identity during embryonic development requires precise spatiotemporal coordination of gene expression. Many transcription factors required for the development of organs have been identified and their expression patterns are known; however, the mechanisms through which they coordinate gene expression in time remain poorly understood. Here we show that hormone-induced transcription factor Blimp-1 participates in the temporal coordination of tubulogenesis in Drosophila melanogaster by regulating the expression of many genes involved in tube maturation. In particular, we demonstrate that Blimp-1 regulates the expression of genes involved in chitin deposition and F-actin organization. We show that Blimp-1 is involved in the temporal control of lumen maturation by regulating the beginning of chitin deposition. We also report that Blimp-1 represses a variety of genes involved in tracheal maturation. Finally, we reveal that the kinase Btk29A serves as a link between Blimp-1 transcriptional repression and apical extra-cellular matrix organization.

developmental biology↗

bioRxiv2018

Dietary lipids modulate Notch signaling and influence adult intestinal development and metabolism in Drosophila

Tissue homeostasis is a complex balance of developmental signals and environmental cues that dictate stem cell function. However, it remains poorly understood how nutrients interface with developmental pathways. Using the Drosophila midgut as a model we found that during the first four days of adult life, dietary lipids including cholesterol, determine how many enteroendocrine (ee) cells differentiate and persist in the posterior midgut where lipids are preferentially absorbed. The nuclear hormone receptor Hr96 which functions to control sterol trafficking, storage, and utilization, is required for sterol-mediated changes in ee number. Dietary cholesterol influences new intestinal epithelial cell differentiation from stem cells by altering the level and persistance of Notch signaling. Exogenous lipids modulate signaling by changing the stability of the Delta ligand and Notch intracellular domain and their trafficking in endosomal vesicles. Lipid-modulated Notch signaling occurs in other nutrient-dependent tissues such as the ovary, suggesting that Delta trafficking in many cells is sensitive to cellular sterol levels. These diet-mediated alterations in ee number in young animals contribute to a metabolic program adapted to the prevailing nutrient environment that persists after the diet changes. A low sterol diet also slows the proliferation of enteroendocrine tumors initiated by disruptions in the Notch pathway. These studies show that a specific dietary nutrient can modify a key intercellular signaling pathway to shift stem cell differentiation and cause lasting changes in tissue structure and physiology.

developmental biology↗

bioRxiv2018

Capn5 expression in the healthy and regenerating zebrafish retina

PurposeAutosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV) is a devastating inherited autoimmune disease of the eye that displays features commonly seen in other eye diseases, such as retinitis pigmentosa and diabetic retinopathy. ADNIV is caused by a gain of function mutation in Calpain-5 (CAPN5), a calcium dependent cysteine protease. Very little is known about the normal function of Capn5 in the adult retina, and there are conflicting results regarding its role during mammalian embryonic development. The zebrafish (Danio rerio) is an excellent animal model for studying vertebrate development and tissue regeneration, and represents a novel model to explore the function of Capn5 in the eye.\n\nMethodsWe characterized the expression of Capn5 in the developing zebrafish central nervous system (CNS) and retina, in the adult zebrafish retina, and in response to photoreceptor degeneration and regeneration using whole mount in situ hybridization, fluorescent in situ hybridization (FISH), and immunohistochemistry.\n\nResultsIn zebrafish, capn5 is strongly expressed in the developing embryonic brain, early optic vesicles, and in newly differentiated retinal photoreceptors. We found that expression of capn5 co-localized with cone specific markers in the adult zebrafish retina. We observed an increase in expression of Capn5 in a zebrafish model of chronic rod photoreceptor degeneration and regeneration. Acute light damage to the zebrafish retina, was accompanied by an increase in expression of Capn5 in the surviving cones and in a subset of Muller glia.\n\nConclusionsThese studies suggest that Capn5 may play a role in CNS development, photoreceptor maintenance, and photoreceptor regeneration.

developmental biology↗

bioRxiv2018

Efficient expression of genes in the Drosophila germline using a UAS-promoter free of interference by Hsp70 piRNAs

Controlling the expression of genes using a binary system involving the yeast GAL4 transcription factor has been a mainstay of Drosophila melanogaster developmental genetics for twenty-five years. However, most existing GAL4 expression constructs only function effectively in somatic cells, but not in germ cells during oogenesis, for unknown reasons. A special UAS promoter, UASp was created that does express during oogenesis, but the need to use different constructs for somatic and female germline cells has remained a significant technical limitation. Here we show that the expression problem of UASt and many other Drosophila molecular tools in germline cells is caused by their core Hsp70 promoter sequences, which are targeted in female germ cells by Hsp70-directed piRNAs generated from endogenous Hsp70 gene sequences. In a genetic background lacking genomic Hsp70 genes and associated piRNAs, UASt-based constructs function effectively during oogenesis. By reducing Hsp70 sequences targeted by piRNAs, we created UASz, which functions better than UASp in the germline and like UASt in somatic cells.

developmental biology↗

bioRxiv2018

A genome-wide assessment of the ancestral neural crest gene regulatory network

The neural crest is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional profiles and chromatin accessibility of neural crest cells in the basal sea lamprey, in order to gain insight into the ancestral state of the neural crest gene regulatory network (GRN) at the dawn of vertebrates. Transcriptome analyses reveal clusters of co-regulated genes during neural crest specification and migration that show high conservation across vertebrates for dynamic programmes like Wnt modulation during the epithelial to mesenchymal transition, but also reveal novel transcription factors and cell-adhesion molecules not previously implicated in neural crest migration. ATAC-seq analysis refines the location of known cis-regulatory elements at the Hox-2 locus and uncovers novel cis-regulatory elements for Tfap2B and SoxE1. Moreover, cross-species deployment of lamprey elements in zebrafish reveals that the lamprey SoxE1 enhancer activity is deeply conserved, mediating homologous expression in jawed vertebrates. Together, our data provide new insight into the core elements of the GRN that are conserved to the base of the vertebrates, as well as expose elements that are unique to lampreys.

developmental biology↗

bioRxiv2018

Genetically regulated human NODAL splice variants are differentially post-transcriptionally processed and functionally distinct

NODAL is a morphogen essential for early embryonic development in vertebrates. Since much of our understanding of NODAL comes from model organisms, we aimed to directly assess post-transcriptional regulation of human NODAL with specific attention to a newly discovered human-specific NODAL splice variant. Selective depletion of the NODAL variant in human embryonic stem cells resulted in increased LIFR levels, while total NODAL knockdown resulted in a decrease of several markers of pluripotency. The NODAL variant did not transmit a canonical NODAL signal in zebrafish embryos, but may share some functional capability with canonical NODAL in cancer cells. At the protein level, disruption of disulfide bond formation dramatically enhanced proteolytic processing of NODAL. Disruption of NODAL N-glycosylation decreased its secretion but not extracellular stability, and a novel N-glycosylation in the NODAL variant contributed to enhanced secretion. Collectively, this work offers a direct and precise account of post-transcriptional regulation of human NODAL.

developmental biology↗

bioRxiv2018

Transgenerational sterility of small RNA genome silencing mutants in response to germ granule dysfunction

In several species, Piwi/piRNA genome silencing defects lead to immediate sterility accompanied by heterochromatin dysfunction and transposon-induced genomic instability, which may cause Piwi mutant sterility. In C. elegans, Piwi pathway mutants transmit a heritable stress through germ cells that induces sterility after growth for several generations. We found that sterile Piwi pathway mutant germ cells displayed inconsistent increases in DNA damage but consistently altered perinuclear germ granules that are known to promote fertility. Germ granule dysfunction did not elicit transposon expression but was sufficient to induce multiple phenotypes found in sterile Piwi silencing mutants, including germline atrophy and regrowth. Furthermore, loss of the germ granule component PGL-1 accelerated sterility in response to deficiency for prg-1/Piwi. Restoration of germ granule function to sterile pgl-1 mutants restored their fertility. Together, our results suggest that germ granule defects may promote an adult reproductive arrest phenotype that is responsible for Piwi/piRNA mutant sterility.

developmental biology↗

bioRxiv2018

Towards Improving Embryo Selection: Simultaneous Next Generation Sequencing Of DNA And RNA From A Single Trophectoderm Biopsy

Improved embryo selection is crucial in optimizing the results from assisted reproduction. Preimplantation genetic screening reduces time to pregnancy and miscarriages. Correlating the transcriptome of an embryo, with fertility treatments and outcomes, holds promise in improving the overall results. We developed a novel method for embryo selection in fertility treatments that integrates embryonic genomic and transcriptomic data and evaluated it in this pilot study.\n\nA total of 21 embryos donated for research were included. Three were used for the initial development and optimization of sample processing and sequencing. Thereafter, 18 embryos were used to demonstrate the clinical safety and reproducibility of our method. Two trophectoderm biopsies were taken from each embryo: one was processed as a clinical sample for genomic profiling (control, n=18), while the other biopsy (n=18) was split and utilized for independent, simultaneous genomic and transcriptomic analysis, here termed Preimplantation Genetic and Transcriptomic Testing (PGT2).\n\nHigh quality genomic and transcriptomic data were obtained from all analyzed samples. The concordance between genomic data obtained with PGT2 and control samples was 100% with clinical grade quality metrics. Euploid embryos showed downregulation of genes involved in anaerobic metabolism, oxidative phosphorylation, and fatty-acid oxidation. This is the first study to provide full genomic and transcriptomic profiles from a single TE biopsy from human embryos in a clinical setting unleashing the potential of improving embryo selection and outcomes in infertility treatments. Clinical trials are needed to correlate transcriptomic data with outcomes.\n\nSUMMARYDespite advances in assisted reproductive technologies, the success rate has remained relatively constant. Under the age of 35, there is a 40% chance of delivering a child per embryo transfer, which decreases with increasing maternal age. Prioritizing embryos for transfer is based on morphological assessment and, in some cases, incorporates genetic testing as well. Selection of euploid embryos for transfer shortens the time to pregnancy and reduces the risk for miscarriages. Adding the mRNA analysis to the genomic assessment of an embryo has the potential of improving the outcomes of fertility treatments.

developmental biology↗

bioRxiv2018

Intermediate filaments EXC-2 and IFA-4 Maintain Luminal Structure of the Tubular Excretory Canals in Caenorhabditis elegans

The excretory canals of Caenorhabditis elegans are a model for understanding the maintenance of apical morphology in narrow single-celled tubes. Light and electron microscopy shows that mutants in exc-2 start to form canals normally, but these swell to develop large fluid-filled cysts that lack a complete terminal web at the apical surface, and accumulate filamentous material in the canal lumen. Here, whole-genome sequencing and gene rescue show that exc-2 encodes intermediate filament protein IFC-2. EXC-2/IFC-2 protein, fluorescently tagged via CRISPR/Cas9, is located at the apical surface of the canals independently of other intermediate filament proteins. EXC-2 is also located in several other tissues, though the tagged isoforms are not seen in the larger intestinal tube. Tagged EXC-2 binds via pulldown to intermediate filament protein IFA-4, which is also shown to line the canal apical surface. Overexpression of either protein results in narrow but shortened canals. These results are consistent with a model whereby three intermediate filaments in the canals, EXC-2, IFA-4, and IFB-1, restrain swelling of narrow tubules in concert with actin filaments that guide the extension and direction of tubule outgrowth, while allowing the tube to bend as the animal moves.\n\nArticle SummaryThe C. elegans excretory canals form a useful model for understanding formation of narrow tubes. exc-2 mutants start to form normal canals that then swell into fluid-filled cysts. We show that exc-2 encodes a large intermediate filament (IF) protein previously not thought to be located in the canals. EXC-2 is located at the apical (luminal) membrane, binds to another IF protein, and appears to be one of three IF proteins that form a flexible meshwork to maintain the thin canal diameter. This work provides a genetically useful model for understanding the interactions of IF proteins with other cytoskeletal elements to regulate tube size and growth.

developmental biology↗

bioRxiv2018

Spatial and temporal PCP protein dynamics coordinate cell intercalation during neural tube closure

Planar cell polarity (PCP) controls the convergent extension cell movements that drive axis elongation in all vertebrates. Though asymmetric localization of core PCP proteins is central to their function, we currently understand little about PCP protein localization as it relates to the subcellular behaviors that drive convergent extension. Here, we have used high magnification time-lapse imaging to simultaneously monitor cell intercalation behaviors and the localization of the PCP proteins Prickle2 and Vangl2. We observed the expected asymmetric enrichment of PCP proteins, but more interestingly, we also observed tight temporal and spatial correlation of PCP protein enrichment with contractile behavior in cell-cell junctions. These patterns of localization were associated with similar pattern of protein turnover at junctions as assessed by FRAP. In fact, dynamic enrichment of PCP proteins was linked more strongly to junction behavior than to spatial orientation. Finally, recruitment of Prickle2 and Vangl2 to cell-cell junctions was temporally and spatially coordinated with planar polarized oscillations of actomyosin enrichment, and all of these dynamic relationships were disrupted when PCP signaling was manipulated. Together, these results provide a dynamic and quantitative view of PCP protein localization during convergent extension and suggest a complex and intimate link between the dynamic localization of core PCP proteins, actomyosin assembly, and polarized junction shrinking during cell intercalation of the closing vertebrate neural tube.

developmental biology↗

bioRxiv2018

Developmental origin and morphogenesis of the diaphragm, an essential mammalian muscle

The diaphragm is a mammalian skeletal muscle essential for respiration and for separating the thoracic and abdominal cavities. Development of the diaphragm requires the coordinated development of muscle, muscle connective tissue, tendon, nerves, and vasculature that derive from different embryonic sources. However, defects in diaphragm development are common and the cause of an often deadly birth defect, Congenital Diaphragmatic Hernia (CDH). Here we comprehensively describe the normal developmental origin and complex spatial-temporal relationship between the different developing tissues to form a functional diaphragm using a developmental series of mouse embryos genetically and immunofluorescently labeled and analyzed in whole mount. We find that the earliest developmental events are the emigration of muscle progenitors from cervical somites followed by the projection of phrenic nerve axons from the cervical neural tube. Muscle progenitors and phrenic nerve target the pleuroperitoneal folds (PPFs), transient pyramidal-shaped structures that form between the thoracic and abdominal cavities. Subsequently, the PPFs expand across the surface of the liver to give rise to the muscle connective tissue and central tendon, and the leading edge of their expansion precedes muscle morphogenesis, formation of the vascular network, and outgrowth and branching of the phrenic nerve. Thus development and morphogenesis of the PPFs is critical for diaphragm formation. In addition, our data indicate that the earliest events in diaphragm development are critical for the etiology of CDH and instrumental to the evolution of the diaphragm. CDH initiates prior to E12.5 in mouse and suggests that defects in the early PPF formation or their ability to recruit muscle are an important source of CDH. Also, the recruitment of muscle progenitors from cervical somites to the nascent PPFs is uniquely mammalian and a key developmental innovation essential for the evolution of the muscularized diaphragm.\n\nHighlightsO_LIDiaphragm development begins with emigration of muscle progenitors from cervical somites.\nC_LIO_LIPhrenic nerve axons follow muscle path towards nascent pleuroperitoneal folds (PPFs).\nC_LIO_LIPPFs are the target of muscle migration and phrenic nerve axon projection\nC_LIO_LIPPF expansion precedes and likely directs muscle, nerve, and vasculature development.\nC_LIO_LIEarly defects in PPFs and muscle recruitment are likely a source of CDH.\nC_LI

developmental biology↗

bioRxiv2018

Epidermal YAP Activity Drives Canonical WNT16/β-catenin Signaling to Promote Keratinocyte Proliferation in vitro and in the Murine Skin

The skin constantly self-renews throughout adult life. Wnt/{beta}-catenin signaling plays a key role in promoting keratinocyte proliferation in the hair follicles and in the interfollicular epidermis. A recent report demonstrated that epidermal YAP activity drives {beta}-catenin activation to promote keratinocyte proliferation in the murine skin. However, it remains unclear whether this is caused by paracrine activation of canonical Wnt signaling or through other YAP/{beta}-catenin regulatory interactions. In the present study, we found that XAV939-inhibition of canonical WNT signaling in skin of YAP2-5SA-{Delta}C mice resulted in diminished {beta}-catenin activation, reduced keratinocyte proliferation, and a mitigation of the hyperplastic abnormalities in the interfollicular epidermis, signifying a canonical WNT ligand-dependent mechanism. Our subsequent analyses determined that WNT16 is produced in response to YAP activity in keratinocytes both in vitro and in vivo, and that WNT16 drives HaCaT keratinocyte proliferation via canonical WNT16/{beta}-catenin signaling. We conclude that under normal physiological conditions WNT16 is the paracrine WNT ligand secreted in response to epidermal YAP activity that promotes cell proliferation in the interfollicular epidermis. This study delineates a fundamental YAP-driven mechanism that controls normal skin regeneration, and that may be perturbed in human regenerative disease displaying increased YAP and WNT signaling activity.

developmental biology↗

bioRxiv2018

The neuronal ceroid lipofuscinosis protein, Cln7, regulates neural development from the post-synaptic cell.

The neuronal ceroid lipofuscinoses (NCLs) are a group of fatal, monogenic neurodegenerative disorders with an early onset in infancy or childhood. Despite identification of the genes disrupted in each form of the disease, their normal cellular role and how their deficits lead to disease pathology is not fully understood. Cln7, a major facilitator superfamily domain-containing protein, is affected in a late infantile-onset form of NCL. Using the Drosophila larval neuromuscular junction as a model to study neural development, we demonstrate that Cln7 is required for the normal growth of synapses. In a Cln7 mutant, synapses fail to develop fully leading to reduced function and behavioral changes with dysregulation of TOR activity. Cln7 expression is restricted to the post-synaptic cell and the protein localizes to vesicles immediately adjacent to the post-synaptic membrane. Our data suggest an involvement for Cln7 in regulating trans-synaptic communication.

developmental biology↗

bioRxiv2018

A nuclear hormone receptor and lipid metabolism axis are required for the maintenance and regeneration of reproductive organs

Understanding how stem cells and their progeny maintain and regenerate reproductive organs is of fundamental importance. The freshwater planarian Schmidtea mediterranea provides an attractive system to study these processes because its hermaphroditic reproductive system (RS) arises post-embryonically and when lost can be fully and functionally regenerated from the proliferation and regulation of experimentally accessible stem and progenitor cells. By controlling the function of a nuclear hormone receptor gene (nhr-1), we established conditions in which to study the formation, maintenance and regeneration of both germline and somatic tissues of the planarian RS. We found that nhr-1(RNAi) not only resulted in the gradual degeneration and complete loss of the adult hermaphroditic RS, but also in the significant downregulation of a large cohort of genes associated with lipid metabolism. One of these, Smed-acs-1, a homologue of Acyl-CoA synthetase, was indispensable for the development, maintenance and regeneration of the RS, but not for the homeostasis or regeneration of other somatic tissues. Remarkably, supplementing nhr-1(RNAi) animals with either bacterial Acyl-CoA synthetase or the lipid metabolite Acetyl-CoA rescued the phenotype restoring the maintenance and function of the hermaphroditic RS. Our findings uncovered a likely evolutionarily conserved role for nuclear hormone receptors and lipid metabolism in the regulation of stem and progenitor cells required for the long-term maintenance and regeneration of animal reproductive organs, tissues and cells.

developmental biology↗

bioRxiv2018

Longitudinal single cell fate in hematopoiesis in vivo using cellular barcoding and DiSNE movie visualization

Identifying the progeny of many single progenitor cells simultaneously can be achieved by tagging progenitors with unique heritable DNA barcodes, and allows inferences of lineage relationships, including longitudinally. While this approach has shed new light on single cell fate heterogeneity, data interpretation remains a major challenge. In this study, we applied our developmental interpolated t-Distributed Stochastic Neighbor Embedding (DiSNE) movie approach to visualize the clonal dynamics of hematopoietic reconstitution in primates and identify novel developmental patterns, namely a potential cluster of hematopoietic progenitors with early T cell and later granulocyte production.\n\nKey pointsO_LIComplex single cell haematopoietic fate heterogeneity can be visualized and assessed with tSNE pie maps\nC_LIO_LIDiSNE movie visualization of in vivo haematopoiesis allows \"play back\" of the waves of haematopoiesis\nC_LIO_LIIdentification of novel hematopoietic progenitors with early T cell and later granulocyte production\nC_LI

developmental biology↗

bioRxiv2018

Aneuploidy Promotes Intestinal Dysplasia in Drosophila

Aneuploidy is associated with different human diseases, particularly cancer, but how different cell types within tissues respond to aneuploidy is not fully understood. In some studies, aneuploidy has been shown to have a deleterious effect and lead to cell death, however it has also been shown to be a causal event of tumorigenesis in other contexts.\n\nHere, we show that Drosophila intestinal stem cells have a particular tolerance to aneuploidy and do not activate apoptosis in response to chromosome misegregation like other non-stem cells. Instead, we observe the development of tissue dysplasia characterized by an accumulation of progenitor cells, increased stem cell proliferation rate, and an excess of cells of the enteroendocrine lineage. Our findings highlight the importance of mechanisms acting to prevent aneuploidy within tissue stem cells and provide an in vivo model of how these cells can act as reservoirs for genomic alterations that can lead to dysplasia.

developmental biology↗

bioRxiv2018

4D imaging reveals stage dependent random and directed cell motion during somite morphogenesis

Somites are paired embryonic segments that form in a regular sequence from unsegmented mesoderm during vertebrate development. Of fundamental importance, they are transient structures that generate cell lineages of the musculoskeletal system in the trunk such as cartilage, tendon, bone, endothelial cells and skeletal muscle. Surprisingly, very little is known about the morphological transition and cellular dynamics during somite differentiation. Here, we address this by examining cellular rearrangements and morphogenesis in differentiating somites using live multi photon imaging of GFP-transgenic chick embryos. We specifically focussed on the dynamic changes in two principle regions within the somite (the medial and lateral domains) to investigate extensive morphological changes. Furthermore, by using quantitative analysis and cell tracking, we were able to capture for the first time a progenitor cell bulk movement towards the rostral-medial domain of the myotome, where skeletal muscle formation first initiates.

developmental biology↗

bioRxiv2018

Temporal Control of Transcription by Zelda in living Drosophila embryos

Abstract/introPioneer factors have the exquisite ability to engage their target sites at nucleosomal DNA, which leads to a local remodeling of chromatin and the establishment of a transcriptional competence. However, the direct impact of enhancer priming by pioneer factors on the temporal control of gene expression and on mitotic memory remains elusive. In Drosophila embryos, the maternally deposited activator Zelda (Zld) exhibits key pioneer factor properties and indeed regulates the awakening of the zygotic genome. The analysis of thousands of endogenous Zld bound regions in various genetic contexts, as well as the study of isolated synthetic enhancers with static approaches, led to the proposal that Zld could act as a quantitative developmental timer. Here we employ quantitative live imaging methods and mathematical modeling to directly test the effect of Zld on temporal coordination in gene activation and on mitotic memory. Using an automatic tracking software, we quantified the timing of activation in hundreds of nuclei and their progeny in Drosophila embryos. We demonstrate that increasing the number of Zld binding sites accelerates the kinetics of transcriptional activation regardless of their past transcriptional state. In spite of its known pioneering activities, we show that Zld is not a mitotic bookmarker and is neither necessary nor sufficient to foster mitotic memory. Fluorescent recovery after photo-bleaching and fluorescent correlation spectroscopy experiments reveal that, Zld is highly dynamic and exhibits transient binding to chromatin. We propose that Zld low binding rates could be compensated for by local accumulation of Zld in nuclear microenvironments in vivo, thus allowing rapid and coordinated gene activation.

developmental biology↗