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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

The Spatio-Temporal Control of Zygotic Genome Activation

One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the mid-blastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation, and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal and BMP signaling together generate most of the spatio-temporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.

developmental biology↗

bioRxiv2018

Cadherin switch marks germ layer formation in the diploblastic sea anemone Nematostella vectensis

Morphogenesis is a shape-building process during development of multicellular organisms. During this process the establishment and modulation of cell-cell contacts play an important role. Cadherins, the major cell adhesion molecules, form adherens junctions connecting ephithelial cells. Numerous studies in Bilateria have shown that cadherins are associated with the regulation of cell differentiation, cell shape changes, cell migration and tissue morphogenesis. To date, the role of Cadherins in non-bilaterians is unknown. Here, we study the expression and the function of two paralogous classical cadherins, cadherin1 and cadherin3, in the diploblastic animal, the sea anemone Nematostella vectensis. We show that a cadherin switch is accompanying the formation of germ layers. Using specific antibodies, we show that both cadherins are localized to adherens junctions at apical and basal positions in ectoderm and endoderm. During gastrulation, partial EMT of endodermal cells is marked by a step-wise downregulation of cadherin3 and upregulation of cadherin1. Knockdown experiments show that both cadherins are required for maintenance of tissue integrity and tissue morphogenesis. This demonstrates that cnidarians convergently use cadherins to differentially control morphogenetic events during development.

developmental biology↗

bioRxiv2018

The coordination of terminal differentiation and cell cycle exit is mediated through the regulation of chromatin accessibility

During terminal differentiation most cells will exit the cell cycle and enter into a prolonged or permanent G0. Cell cycle exit is usually initiated through the repression of cell cycle gene expression by formation of a transcriptional repressor complex called DREAM. However when DREAM repressive function is compromised during terminal differentiation, additional unknown mechanisms act to stably repress cycling and ensure robust cell cycle exit. Here we provide evidence that developmentally programmed, temporal changes in chromatin accessibility at a subset of critical cell cycle genes acts to enforce cell cycle exit during terminal differentiation in the Drosophila melanogaster wing. We show that during terminal differentiation, chromatin closes at a set of pupal wing enhancers for the key rate-limiting cell cycle regulators cycE, e2f1 and stg. This closing coincides with wing cells entering a robust postmitotic state that is strongly refractory to cell cycle re-activation. When cell cycle exit is genetically disrupted, chromatin accessibility at cell cycle genes remains largely unaffected and the closing of enhancers at cycE, e2f1 and stg proceeds independent of the cell cycling status. Instead, disruption of cell cycle exit leads to changes in accessibility and expression of a subset of hormone-induced transcription factors involved in the progression of terminal differentiation. Our results uncover a mechanism that acts as a cell cycle-independent timer to limit aberrant cycling in terminally differentiating tissues. In addition, we provide a new molecular description of the cross-talk between cell cycle exit and terminal differentiation during metamorphosis.

developmental biology↗

bioRxiv2018

High temperature limits on developmental canalization in the ascidian Ciona intestinalis

The normal embryogenesis of marine animals is typically confined to a species-specific range of temperatures. Within that temperature range development results in a consistent, or canalized, phenotype, whereas above and below the range abnormal phenotypes are produced. This study reveals an abrupt high temperature limit, occurring over a 1-2{degrees}C range, for normal embryonic development in C. intestinalis. Above that threshold morphological abnormalities in the notochord and other organs are observed, beginning with cleavage and gastrula stages, and becoming more pronounced as embryogenesis proceeds. However, even in highly morphologically abnormal temperature disrupted (TD) embryos, cell type specification, including muscle, endoderm, notochord, and sensory pigment cells is accomplished. An explanation for this finding is that in C. intestinalis cell type specification occurs relatively early in embryogenesis, due to cleavage stage segregation of maternal cytoplasmic determinants and short-range cell interactions, which are largely intact in TD embryos. On the other hand, morphogenesis of the notochord and other structures is dependent on precise cell movement and shape changes after the gastrula stage, which appear to be disrupted above the high temperature threshold. These findings have implications for the relationship between ecology and reproduction in C. intestinalis. More broadly they point to mechanisms behind canalization in animals, such as ascidians, characterized by early, largely autonomous, cell type specification.

developmental biology↗

bioRxiv2018

Wnt/β-catenin signaling is required for the development of multiple nephron segments

The nephron is composed of distinct segments that perform unique physiological functions to generate urine. Little is known about how multipotent nephron progenitor cells differentiate into different nephron segments. It is well known that Wnt/{beta}-catenin signaling regulates the maintenance and commitment of mesenchymal nephron progenitors during kidney development. However, it is not fully understood how it regulates nephron patterning after nephron progenitors undergo mesenchymal-to-epithelial transition. To address this, we performed {beta}-catenin loss-of-function and gain-of-function studies in epithelial nephron progenitors in the mouse kidney. Consistent with a previous report, the formation of the renal corpuscle was defective in the absence of {beta}-catenin. Interestingly, we found that epithelial nephron progenitors lacking {beta}-catenin were able to form presumptive proximal tubules but that they failed to further develop into differentiated proximal tubules, suggesting that Wnt/{beta}-catenin signaling plays a critical role in proximal tubule development. We also found that epithelial nephron progenitors lacking {beta}-catenin failed to form the distal tubules. Constitutive activation of Wnt/{beta}-catenin signaling blocked the proper formation of all nephron segments, suggesting tight regulation of Wnt/{beta}-catenin signaling during nephron patterning. This work shows that Wnt/{beta}-catenin signaling regulates the patterning of multiple nephron segments along the proximo-distal axis of the mammalian nephron.

developmental biology↗

bioRxiv2018

Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome

Kabuki Syndrome patients have a spectrum of congenital disorders, including congenital heart defects, the primary determinant of mortality. Seventy percent of Kabuki Syndrome patients have mutations in the histone methyl-transferase KMT2D. However, the underlying mechanisms that drive these congenital disorders are unknown. Here, we generated and characterized a zebrafish kmt2d null mutant that recapitulates the cardinal phenotypic features of Kabuki Syndrome, including microcephaly, palate defects, abnormal ear development and cardiac defects. The cardiovascular defects consist of abnormal aortic arches and hypoplastic ventricle, driven by previously unknown aberrant endocardial and endothelial vasculogenesis. We identify a regulatory link between the Notch pathway and Kmt2d during vasculogenesis and show that pharmacological inhibition of Notch signaling rescues the cardiovascular phenotype in zebrafish Kabuki Syndrome. Taken together these findings demonstrate that Kmt2d regulates vasculogenesis, provide evidence for interactions between Kmt2d and Notch signaling in Kabuki Syndrome, and suggest future directions for clinical research.

developmental biology↗

bioRxiv2018

Discovery of antimicrobial compounds from Lendenfeldia, Ircinia and Dysidea sponges using bioassay guided fractionation of marine extracts

Multidrug resistant bacteria have emerged as a threat to public health all over the world. At the same time, the discovery of new bioactive small molecules with antimicrobial activity and suitable pharmacological properties has waned. Herein we report the screening of marine extracts to identify novel compounds with antimicrobial activity. Bioassay guided fractionation has enabled the discovery and identification of a family of simple amines with promising activity against methicillin resistant Staphylococcus aureus (MRSA). To confirm the natural product structures proposed, these compounds and analogues have been prepared synthetically. Several of the synthetic analogues showed promising bioactivity against the medically important pathogens MRSA (MICs to 12.5 {micro}M), Mycobacterium tuberculosis (MICs to 0.02 {micro}M), uropathogenic Escherichia coli (MIC 6.2 {micro}M) and Pseudomonas aeruginosa (MIC 3.1 {micro}M). Cross-referencing antimicrobial activity and toxicity show that these synthetic compounds display a favourable therapeutic index for their target pathogens.

developmental biology↗

bioRxiv2018

Targeted genomic integration of EGFP under tubulin beta 3 class III promoter and mEos2 under tryptophan hydroxylase 2 promoter does not produce sufficient levels of reporter gene expression

Neuronal tracing is a modern technology that is based on the expression of fluorescent proteins under the control of cell type-specific promoters. However, random genomic integration of the reporter construct often leads to incorrect spatial and temporal expression of the marker protein. Targeted integration (or knock-in) of the reporter coding sequence is supposed to provide better expression control by exploiting endogenous regulatory elements. Here we describe the generation of two fluorescent reporter systems: EGFP under pan-neural marker class III {beta}-tubulin (Tubb3) promoter and mEos2 under serotonergic neuron specific tryptophan hydroxylase 2 (Tph2) promoter. Differentiation of Tubb3-EGFP ES cells into neurons revealed that though Tubb3-positive cells express EGFP, its expression level is not sufficient for the neuronal tracing by routine fluorescent microscopy. Similarly, the expression levels of mEos2-TPH2 in differentiated ES cells was very low and could be detected only on mRNA level using PCR-based methods. Our data shows that the use of endogenous regulatory elements to control transgene expression is not always beneficial compared to random genomic integration.

developmental biology↗

bioRxiv2018

Discovery of Alstrom syndrome gene as a regulator of centrosome duplication in asymmetrically dividing stem cells in Drosophila.

Stereotypical inheritance of the mother vs. daughter centrosomes has been reported in several stem cells that divide asymmetrically. We report the identification of a protein that exhibits asymmetric localization between mother and daughter centrosomes in asymmetrically dividing Drosophila male germline stem cells (GSCs). We show that Alms1a, a Drosophila homolog of the causative gene for the human ciliopathy Alstrom Syndrome, is a ubiquitous mother centriole protein with a unique additional localization to the daughter centriole only in the mother centrosome of GSCs. Depletion of alms1a results in rapid loss of centrosomes due to failure in daughter centriole duplication. We reveal that alms1a is specifically required for centriole duplication in asymmetrically dividing cells but not in symmetrically dividing differentiating cells in multiple stem cell lineages. The unique requirement of alms1a in asymmetric dividing cells may shed light onto the molecular mechanisms of Alstrom syndrome pathogenesis.

developmental biology↗

bioRxiv2018

Symmetry breaking in the embryonic skin triggers a directional and sequential front of competence during plumage patterning

The development of an organism involves the formation of patterns from initially homogeneous surfaces in a reproducible manner. Simulations of various theoretical models recapitulate final states of natural patterns1-4 yet drawing testable hypotheses from those often remains difficult4,5. Consequently, little is known on pattern-forming events. Here, we extend modeling to reproduce not only the final plumage pattern of birds, but also the observed natural variation in its dynamics of emergence in five species. We built a unified model intrinsically generating the directionality, sequence, and duration of patterning, and used in vivo experiments to test its parameter-based predictions. We showed that while patterning duration is controlled by overall cell proliferation, its directional and sequential progression result from a pre-pattern: an initial break in surface symmetry launches a traveling front of increased cell density that defines domains with self-organizing capacity. These results show that universal mechanisms combining pre-patterning and self-organization govern the timely emergence of the plumage pattern in birds.

developmental biology↗

bioRxiv2018

Embryo geometry drives formation of robust signaling gradients through receptor localization

Morphogen signals are essential for cell fate specification during embryogenesis. Some receptors that sense these morphogen signals are known to localize to only the apical or basal membrane of polarized cell lines in vitro. How such localization affects morphogen sensing and patterning in the developing embryo remains unknown. Here, we show in the early mouse embryo that the formation of a robust BMP signaling gradient depends on restricted, basolateral localization of the BMP receptors. Mis-localizing these receptors to apical membrane leads to ectopic BMP signaling in vivo in the mouse embryo. To reach the basolaterally localized receptors in epiblast, BMP4 ligand, secreted by the extra-embryonic ectoderm, has to diffuses through the narrow interstitial space between the epiblast and the underlying endoderm. This restricted, basolateral diffusion creates a signaling gradient. The embryo geometry further buffers the gradient from fluctuations in the levels of BMP4. Our results demonstrate the importance of receptor localization and embryo geometry in shaping morphogen signaling during embryogenesis.

developmental biology↗

bioRxiv2018

In vivo epigenetic editing of sema6a promoter reverses impaired transcallosal connectivity caused by C11orf46/ARL14EP neurodevelopmental risk gene

Many neuropsychiatric risk genes contribute to epigenetic regulation of gene expression but very little is known about specific chromatin-associated mechanisms governing the formation and maintenance of neuronal connectivity. Here we show that transcallosal connectivity is critically dependent on C11orf46 (also known as ARL14EP), a small nuclear protein encoded in the chromosome 11p13 Wilms Tumor, Aniridia, Genitourinary Abnormalities, intellectual disability (formerly referred to as Mental Retardation) (WAGR) risk locus. C11orf46 haploinsufficiency in WAGR microdeletion cases was associated with severe hypoplasia of the corpus callosum. In utero short hairpin RNA-mediated C11orf46 knockdown disrupted transcallosal projections of cortical pyramidal neurons, a phenotype that was rescued by wild type C11orf46 but not the C11orf46R236H mutant associated with autosomal recessive intellectual disability. Multiple genes encoding key regulators of axonal growth and differentiation, including Sema6A, were hyperexpressed in C11orf46-knockdown neurons. Importantly, RNA-guided epigenetic editing of neuronal Sema6a gene promoters via a dCas9 protein-conjugated SunTag scaffold with multimeric (10x) C11orf46 binding during early developmental periods, resulted in normalization of expression and rescue of transcallosal dysconnectivity via repressive chromatin remodeling, including up-regulated histone H3K9 methylation by the KAP1-SETDB1 repressor complex. Our study demonstrates that interhemispheric communication is highly sensitive to locus-specific remodeling of neuronal chromatin, revealing the therapeutic potential for shaping the brains connectome via gene-targeted designer activators and repressor proteins.

developmental biology↗

bioRxiv2018

Homeostatic and tumourigenic activity of SOX2+ pituitary stem cells is controlled by the LATS/YAP/TAZ cascade

SOX2 positive pituitary stem cells (PSCs) are specified embryonically and persist throughout life, giving rise to all pituitary endocrine lineages. We have previously shown the activation of the MST/LATS/YAP/TAZ signalling cascade in the developing and postnatal mammalian pituitary. Here, we investigate the function of this pathway during pituitary development and in the regulation of the SOX2 cell compartment. Through loss- and gain-of-function genetic approaches, we reveal that restricting YAP/TAZ activation during development is essential for normal organ size and specification from SOX2+ PSCs. Postnatal deletion of LATS kinases and subsequent upregulation of YAP/TAZ leads to uncontrolled clonal expansion of the SOX2+ PSCs and disruption of their differentiation, causing the formation of non-secreting, aggressive pituitary tumours. In contrast, sustained expression of YAP alone results in expansion of SOX2+ PSCs capable of differentiation and devoid of tumourigenic potential. Our findings identify the LATS/YAP/TAZ signalling cascade as an essential component of PSC regulation in normal pituitary physiology and tumourigenesis.

developmental biology↗

bioRxiv2018

Netrin/UNC-6 triggers actin assembly and non-muscle myosin activity to drive dendrite retraction in the self-avoidance response.

Dendrite growth is constrained by the self-avoidance response but the downstream pathways that balance these opposing mechanisms are unknown. We have proposed that the diffusible cue UNC-6(Netrin) is captured by UNC-40 (DCC) for a short-range interaction with UNC-5 to trigger self-avoidance in the C. elegans PVD neuron. Here we report that the actin-polymerizing proteins UNC-34(Ena/VASP), WSP-1(WASP), UNC-73(Trio), MIG-10(Lamellipodin) and the Arp2/3 complex effect dendrite retraction in the self-avoidance response mediated by UNC-6(Netrin). The paradoxical idea that actin polymerization results in shorter rather than longer dendrites is explained by our finding that NMY-1 (non-muscle myosin II) is necessary for retraction and could therefore mediate this effect in a contractile mechanism. Our results also show that dendrite length is determined by the antagonistic effects on the actin cytoskeleton of separate sets of effectors for retraction mediated by UNC-6(Netrin) versus outgrowth promoted by the DMA-1 receptor. Thus, our findings suggest that the dendrite length depends on an intrinsic mechanism that balances distinct modes of actin assembly for growth versus retraction.

developmental biology↗

bioRxiv2018

Satellite DNA-containing gigantic introns in a unique gene expression program during Drosophila spermatogenesis

Intron gigantism, where genes contain megabase-sized introns, is observed across species, yet little is known about its purpose or regulation. Here we identify a unique gene expression program utilized for the proper expression of genes with intron gigantism. We find that two Drosophila genes with intron gigantism, kl-3 and kl-5, are transcribed in a spatiotemporal manner over the course of spermatocyte differentiation, which spans ~90 hours. The introns of these genes contain megabases of simple satellite DNA repeats that comprise over 99% of the gene loci, and these satellite-DNA containing introns are transcribed. We identify two RNA-binding proteins that specifically localize to kl-3 and kl-5 transcripts and are needed for the successful transcription or processing of these genes. We propose that genes with intron gigantism require a unique gene expression program, which may serve as a platform to regulate gene expression during cellular differentiation.

developmental biology↗

bioRxiv2018

General characterization of regeneration in Aeolosoma viride

Regeneration has long attracted scientists for its potential to restore lost, damaged or aged tissues and organs. A wide range of studies have conducted on different model organisms on both cellular and molecular levels. Current evidences suggest that a variety of regenerative strategies are developed and used by different species, and their regenerative strategies are highly correlated to their reproductive methods. Our present work focused on the freshwater annelid Aeolosoma viride, which reproduces by paratonic fission and is capable of complete regeneration. We found out that A. viride can regenerate both anterior and posterior end, even with only 3 segments remained. This process is characterized by epimorphosis that involves large amount of cell proliferation which drives the formation of blastema. Cell proliferation and regeneration successful ratio were significantly decreased when treated with microtubule inhibitor taxol or Avi-tubulin dsRNA, which confirmed that cell proliferation served as a key event during regeneration. Together, our data described the regenerative processes of A. viride, which includes high level of cell proliferation and the formation of blastema. Furthermore, our findings demonstrated A. viride as a potential model for the study of regeneration.

developmental biology↗

bioRxiv2018

Dissection of intestines from larval zebrafish for molecular analysis

Epigenetic data obtained from whole zebrafish embryos or larvae may mask or dilute organ-specific information. Fluorescence activated cell sorting can diverge cells from their native state, and cryosections often yield insufficient material for molecular analysis. Here, we present a reproducible method for larval intestinal isolation at 5, 7, and 9 days post-fertilization, using the intestine-specific transgene tgBAC(cldn15la:GFP). With tweezers, the intestine can be pulled out of the abdomen in one smooth motion. Upon removal of adhering tissues, intestines can be directly used for analyses. Each dissection takes 3-6 minutes per fish. We demonstrate that 10 and 25 dissected intestines yield enough material for RNA-sequencing and ChIP-sequencing, respectively. This method results in high quality, live material, suitable for many downstream applications.\n\nMETHOD SUMMARYWe present a reproducible method for zebrafish larval intestinal isolation which results in high quality, live material. With tweezers, the intestine can be pulled out of the abdomen and after removal of adhering tissues, intestines can be directly used for analyses. We demonstrate that 10 and 25 dissected intestines yield enough material for RNA-sequencing and ChIP-sequencing, respectively.

developmental biology↗

bioRxiv2018

Bioinformatic screening of genes present only in well regenerating vertebrates reveals novel FGF and purinergic signaling modulator - c-Answer

The genetic basis of higher regenerative capacity of fishes, amphibians and reptiles compared to birds and mammals is still poorly understood. Though it is thought to be a result of restructuring in the regulatory network of a static set of genes, we argued that it could be due to the loss of genes essential for regeneration. In the present work, we formulate a bioinformatic approach to systematic search for the such genes. Having identified them, we further investigated one we dubbed \"c-Answer\", which encodes a membrane protein, regulating the regeneration of body appendages and the telencephalic development through binding to FGFR and P2Y1 receptors and promoting MAPK/ERK and purinergic signaling. The obtained data suggest that elimination of c-Answer in the ancestors of warm-blooded animals conditioned the decreased activity of at least two signaling pathways, which in turn could contribute to changes in mechanisms that regulate the forebrain development and regeneration.

developmental biology↗