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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 91 records · Page 5Linked to original sources

bioRxiv2017

A novel flatworm-specific gene family implicated in reproduction in Macrostomum lignano

Free-living flatworms, such as the planarian Schmidtea mediterranea, are extensively used as model organisms to study stem cells and regeneration. The majority of studies in planarians so far focused on broadly conserved genes. However, investigating what makes these animals different might be equally informative for understanding its biology. Here, we present a re-analysis of neoblast and germline transcriptional signatures in the flatworm M. lignano and combine it with the whole-animal electron microscopy atlas (nanotomy) as a reference platform for ultrastructural studies in M. lignano. We show that germline-enriched genes have a high fraction of flatworm-specific genes and identify Mlig-sperm1 gene as a member of a novel gene family conserved only in free-living flatworms and essential for producing healthy spermatozoa. This work demonstrates that investigation of flatworm-specific genes is crucial for understanding flatworm biology and establishes a basis for future research in this direction in M. lignano.

developmental biology↗

bioRxiv2018

Embryo timelapses can be compiled and quantified to understand canonical histone dynamics across multiple cell cycles.

In the last decade, computational analysis of big datasets has facilitated the processing of unprecedented quantities of collected biological data. Thus, automations and big data analyses have been revolutionary in detecting and quantifying subtle phenotypes in cell biological contexts. Analyzing similar quantities of data in larger and more complicated biological systems such as live embryos has been more challenging due to experimental necessities impeding both compilations of data collection and informative analysis. Here we present a streamlined workflow that can quantify cell cycle dynamics in early developing embryos using fluorescently labeled proteins. We benchmark this pipeline using Caenorhabditis elegans (nematode) embryonic development and a fluorescently labeled histone. Using our pipeline, we find that histone proteins are broadly stable in early embryonic development. In sum, we have utilized the large biological and experimental variation associated with quantification of fluorescent proteins in embryonic systems, to quantify nuclear accumulation rate, chromatin incorporation, and turnover/stability of canonical histones during early development.

developmental biology↗

bioRxiv2018

Acidic microenvironment shaped by lactate accumulation promotes pluripotency through multiple mechanisms

Enhanced glycolysis is a distinct feature associated with numerous stem cells and cancer cells. However, little is known about its regulatory roles in gene expression and cell fate determination. Here we show that acidic environment shaped by lactate accumulation promotes the self-renewal and pluripotency of both mouse and human embryonic stem cells (ESCs). Mechanistically, acidic pH reduces the tri-methylation of H3K27 globally at transcriptional start sites to partially prevent ESC differentiation. In addition, acidic pH stabilizes a large number of mRNAs including pluripotency genes. Furthermore, we found that AGO1 protein is downregulated at acidic conditions, leading to the de-repression of a subset of microRNA targets in low-pH treated ESCs. Altogether, our study provides insights into mechanisms whereby acidic microenvironment produced by enhanced glycolysis regulates gene expression to determine cell fate and has broad implications in the fields of regenerative medicine and cancer biology.

developmental biology↗

bioRxiv2017

Morphometrics of complex cell shapes: Lobe Contribution Elliptic Fourier Analysis (LOCO-EFA)

Quantifying cell morphology is fundamental to the statistical study of cell populations, and can help us unravel mechanisms underlying cell and tissue morphogenesis. Current methods, however, require extensive human intervention, are highly sensitive to parameter choice, or produce metrics that are difficult to interpret biologically. We therefore developed a novel method, Lobe Contribution Elliptical Fourier Analysis (LOCO-EFA), which generates from digitalised cell outlines meaningful descriptors that can be directly matched to morphological features. We show that LOCO-EFA provides a tool to phenotype efficiently and objectively populations of cells by applying it to the complex shaped pavement cells of Arabidopsis thaliana wild type and speechless leaves. To further validate our method, we analysed computer-generated tissues, where cell shape can be specified in a controlled manner. LOCO-EFA quantifies deviations between the specified shape that an individual in silico cell takes up when in isolation and the resultant shape when they are allowed to interact within a confluent tissue, thereby assessing the role of cell-cell interactions on population cell shape distributions.\n\nSummary statement\n\nNovel method (LOCO-EFA) quantifies complex cell shapes, extracting meaningful biological features such as protrusion number and amplitude; here shown for plant pavement cells and validated on in silico tissues.

developmental biology↗

bioRxiv2017

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast

Single-cell profiling techniques create opportunities to delineate cell fate progression in mammalian development. Recent studies provide transcriptome data from human preimplantation embryos, in total comprising nearly 2000 individual cells. Interpretation of these data is confounded by biological factors such as variable embryo staging and cell-type ambiguity, as well as technical challenges in the collective analysis of datasets produced with different sample preparation and sequencing protocols. Here we address these issues to assemble a complete gene expression time course spanning human preimplantation embryogenesis. We identify key transcriptional features over developmental time and elucidate lineage-specific regulatory networks. We resolve post hoc cell-type assignment in the blastocyst, and define robust transcriptional prototypes that capture epiblast and primitive endoderm lineages. Examination of human pluripotent stem cell transcriptomes in this framework identifies culture conditions that sustain a naive state pertaining to the inner cell mass. Our approach thus clarifies understanding both of lineage segregation in the early human embryo and of in vitro stem cell identity, and provides an analytical resource for comparative molecular embryology.

developmental biology↗

bioRxiv2018

Increased PHGDH expression uncouples hair follicle cycle progression and promotes inappropriate melanin accumulation

Copy number gain of the PHGDH gene that encodes the first enzyme of the serine biosynthesis pathway is found in some human cancers, including a subset of melanomas. In order to study the effect of increased PHGDH expression in tissues in vivo, we generated mice harboring a PHGDHtetO allele that allows tissue-specific, doxycycline-inducible PHGDH expression. Tissues and cells derived from PHGDHtetO mice exhibit increased serine biosynthesis. Histological examination of skin tissue from PHGDHtetO mice reveals the presence of melanin granules in anagen II hair follicles, despite the fact that melanin synthesis is normally closely coupled to the hair follicle cycle and does not begin until later in the cycle. This phenotype occurs in the absence of any global change in hair follicle cycle timing. The inappropriate presence of melanin early in the hair follicle cycle following PHGDH expression is also accompanied by increased melanocyte abundance in anagen II skin. Together, these data support a model in which PHGDH expression affects melanocyte proliferation and/or differentiation and may provide insight into how PHGDH expression impacts normal melanocyte biology to promote melanoma.\n\nSIGNIFICANCEThe significance behind copy number gain of PHGDH in human cancers is unclear. In this study, we generate a mouse model that mimics PHGDH gene copy number gain and characterize its effect on normal tissues. Increased PHGDH expression yields a phenotype of aberrant melanin production, which indicates that PHGDH expression may play a role in normal melanocyte biology. This result may provide insight into why PHGDH copy number gain is observed in melanoma more frequently than in most other tumor types.

developmental biology↗

bioRxiv2017

GDF15 Concentrations in Maternal Serum Associated with Vomiting in Pregnancy: the Cambridge Baby Growth Study

Nausea and vomiting in pregnancy (NVP) affects 70-90% of all pregnant women but its pathogenesis is unknown. Growth and Differentiation Factor 15 (GDF15), secreted from the trophoblast and decidual stromal cells, is present at high levels in the blood of pregnant women. The receptor for GDF15 has recently been identified and is specifically expressed in the hindbrain where it transmits aversive signals including nausea and conditioned taste aversion. We explored the relationship between GDF15 concentrations in maternal serum during pregnancy and self-reported NVP. In a study of 791 women from the Cambridge Baby Growth Study maternal GDF15 concentrations were higher in women who reported vomiting in the 2nd trimester (geometric mean: 11,670 pg/mL; 95% confidence interval: 11,056-12,318) and were even higher in the eleven women who reported taking anti-emetics during pregnancy (13,376 (10,821-16,535) compared to those who reported no nausea or vomiting during pregnancy (10,657 (10,121-11,222); P=0.02 and P=0.04, respectively, adjusted for gestational age at sampling and maternal BMI). In conclusion serum GDF15 concentrations early in the second trimester of pregnancy are significantly and positively associated with second trimester vomiting and with maternal anti-emetic use. In the context of the recently revealed biology of GDF15 this data suggests that antagonism of GDF15 may have some potential for therapeutic benefit in NVP.

developmental biology↗

bioRxiv2018

Extracellular Vesicle-delivered Bone Morphogenetic Proteins: A novel paracrine mechanism during embryonic development

Morphogens including Wnt, Hedgehog and BMP proteins are essential during embryonic development and early induction of organ progenitors. Besides free diffusion to form signalling gradients, extracellular vesicle- (EV-) mediated morphogen transport was identified as a central mechanism for Wnt- and Hh-signalling. Here, we investigated EVs isolated from whole zebrafish embryos as a potential morphogen transport mechanism. Inhibition of EV-secretion during development leads to severe dorsalization phenotypes, reminiscent of disrupted BMP-signalling. Subsequently, we found that EVs isolated from zebrafish embryos at bud stage contain biologically active BMP2/4 protein. Embryos with inhibited EV secretion display reduced Smad1/5/9-phosphorylation and downstream gene expression activity. We further show that BMP-containing EVs are secreted by endodermal cells in vitro, and inhibition of endodermal-EV release in vivo causes signs of BMP signalling loss. Our data provides evidence that establishes the transport of BMP2/4 by EVs as an essential but so far undiscovered mechanism in developmental morphogenesis.

developmental biology↗

bioRxiv2017

Cardiac directed differentiation using small molecule Wnt modulation at single-cell resolution

Differentiation into diverse cell lineages requires the orchestration of gene regulatory networks guiding diverse cell fate choices. Utilizing human pluripotent stem cells, we measured expression dynamics of 17,718 genes from 43,168 cells across five time points over a thirty day time-course of in vitro cardiac-directed differentiation. Unsupervised clustering and lineage prediction algorithms were used to map fate choices and transcriptional networks underlying cardiac differentiation. We leveraged this resource to identify strategies for controlling in vitro differentiation as it occurs in vivo. HOPX, a non-DNA binding homeodomain protein essential for heart development in vivo was identified as dys-regulated in in vitro derived cardiomyocytes. Utilizing genetic gain and loss of function approaches, we dissect the transcriptional complexity of the HOPX locus and identify the requirement of hypertrophic signaling for HOPX transcription in hPSC-derived cardiomyocytes. This work provides a single cell dissection of the transcriptional landscape of cardiac differentiation for broad applications of stem cells in cardiovascular biology.

developmental biology↗

bioRxiv2018

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

Cell lineages provide the framework for understanding how multicellular organisms are built and how cell fates are decided during development. Describing cell lineages in most organisms is challenging, given the number of cells involved; even a fruit fly larva has ~50,000 cells and a small mammal has more than 1 billion cells. Recently, the idea of using CRISPR to induce mutations during development as heritable markers for lineage reconstruction has been proposed and trialled by several groups. While an attractive idea, its practical value depends on the accuracy of the cell lineages that can be generated by this method. Here, we use computer simulations to estimate the performance of this approach under different conditions. Our simulations incorporate empirical data on CRISPR-induced mutation frequencies in Drosophila. We show significant impacts from multiple biological and technical parameters - variable cell division rates, skewed mutational outcomes, target dropouts and different mutation sequencing strategies. Our approach reveals the limitations of recently published CRISPR recorders, and indicates how future implementations can be optimised to produce accurate cell lineages.

developmental biology↗

bioRxiv2018

Deterministic Nature of Cellular Position Noise During C. elegans Embryogenesis

Individuals with identical genotypes exhibit great phenotypic variability known as biological noise, which has broad implications. While molecular-level noise has been extensively studied, in-depth analysis of cellular-level noise is challenging. Here, we present a systems-level quantitative and functional analysis of noise in cellular position during embryogenesis, an important phenotype indicating differentiation and morphogenesis. We show that cellular position noise is deterministic, stringently regulated by intrinsic and extrinsic mechanisms. The noise level is determined by cell lineage identity and is coupled to developmental properties including embryonic localization, cell contact, and left-right symmetry. Cells follow a concordant low-high-low pattern of noise dynamics, and fate specification triggers a global down-regulation of noise that provide a noise-buffering strategy. Noise is stringently regulated throughout embryogenesis, especially during cell division and cell adhesion and gap junctions function to restrict noise. Collectively, our study reveals system properties and regulatory mechanisms of cellular noise control during development.

developmental biology↗

bioRxiv2018

Stage-specific transcriptomes and DNA methylomes indicate an early and transient loss of transposon control in Arabidopsis shoot stem cells

In contrast to animals, postembryonic development in plants is modular, and aerial organs originate from stem cells in the center of the shoot apical meristem (SAM) throughout life. Descendants of SAM stem cells in the subepidermal layer (L2) give also rise to male and female gametes (reviewed in 1) and are therefore considered primordial germ cells. In these cells, transmission of somatic mutations including virus and TE insertions must be avoided. Despite their essential role for plant development and intergenerational continuity, no comprehensive molecular analysis of SAM stem cells exists, due to their low number, deep embedding among non-stem cells, and difficult isolation. Here we present a comprehensive analysis of stage-specific gene expression and DNA methylation dynamics in Arabidopsis SAM stem cells. Stem cell expression signatures are mostly defined by development, but we also identified a core set of differentially expressed stemness genes. Surprisingly, vegetative SAM stem cells showed increased expression of transposable elements (TEs) relative to surrounding cells, despite high expression of genes connected to epigenetic silencing. We also find increasing methylation at CHG and a drop in CHH methylation at TEs before stem cells enter the reproductive lineage, indicating an onset of epigenetic reprogramming at an early stage. Transiently elevated TE expression is reminiscent of that in animal primordial germ cells (PGCs) 2 and demonstrates commonality of transposon biology. Our results connect SAM stem cells with germline development and transposon evolution and will allow future experiments to determine the degree of epigenetic heritability between generations.

developmental biology↗

bioRxiv2016

From cytoskeletal dynamics to organ asymmetry: a non-linear, regulative pathway underlies left-right patterning

Consistent left-right asymmetry is a fundamental aspect of the bodyplan across phyla, and errors of laterality form an important class of human birth defects. Its molecular underpinning was first discovered as a sequential pathway of left-and right-sided gene expression that controlled positioning of the heart and visceral organs. Recent data have revised this picture in two important ways. First, the physical origin of chirality has been identified; cytoskeletal dynamics underlie the asymmetry of single cell behavior and of patterning of the left-right axis. Second, the pathway is not linear: early disruptions that alter the normal sidedness of upstream asymmetric genes do not necessarily induce defects in the laterality of the downstream genes or in organ situs. Thus, the LR pathway is a unique example of two fascinating aspects of biology: the interplay of physics and genetics in establishing large-scale anatomy, and regulative (shape-homeostatic) pathways that correct errors of patterning over time. Here, we review aspects of asymmetry from its intracellular, cytoplasmic origins to the recently-uncovered ability of the LR control circuitry to achieve correct gene expression and morphology despite reversals of key \"determinant\" genes. We provide novel functional data, in Xenopus laevis, on conserved elements of the cytoskeleton that drive asymmetry, and repair of downstream gene expression anomalies over developmental time. LR patterning can thus serve as a paradigm of how subcellular physics and gene expression cooperate to achieve developmental robustness of a body axis.

Developmental Biology↗

bioRxiv2016

Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls

Axolotls are unique in their ability to regenerate the spinal cord. However, the mechanisms that underlie this phenomenon remain poorly understood. Previously, we showed that resting stem cells in the axolotl spinal cord revert to a molecular state resembling embryonic neuroepithelial cells and functionally acquire rapid proliferative divisions during regeneration. Here we refine in space and time this increase in cell proliferation during regeneration, and identify a dynamic high-proliferation zone in the regenerating spinal cord. By tracking sparsely-labeled cells, we quantify cell influx into the regenerate. Taking a mathematical modelling approach, we integrate these quantitative biological datasets across cellular and tissue level to provide a mechanistic and quantitative understanding of regenerative spinal cord outgrowth. We find that the acceleration of the cell cycle is necessary and sufficient to drive the outgrowth of the regenerating spinal cord in axolotls.

Developmental Biology↗

bioRxiv2018

Molecular recording of mammalian embryogenesis

Understanding the emergence of complex multicellular organisms from single totipotent cells, or ontogenesis, represents a foundational question in biology. The study of mammalian development is particularly challenging due to the difficulty of monitoring embryos in utero, the variability of progenitor field sizes, and the indeterminate relationship between the generation of uncommitted progenitors and their progression to subsequent stages. Here, we present a flexible, high information, multi-channel molecular recorder with a single cell (sc) readout and apply it as an evolving lineage tracer to define a mouse cell fate map from fertilization through gastrulation. By combining lineage information with scRNA-seq profiles, we recapitulate canonical developmental relationships between different tissue types and reveal an unexpected transcriptional convergence of endodermal cells from extra-embryonic and embryonic origins, illustrating how lineage information complements scRNA-seq to define cell types. Finally, we apply our cell fate map to estimate the number of embryonic progenitor cells and the degree of asymmetric partitioning within the pluripotent epiblast during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems to facilitate a quantitative framework for describing developmental processes.

developmental biology↗

bioRxiv2017

Intrauterine position probabilities in mice, rats and gerbils

The position of a developing embryo or foetus relative to members of the same or opposite sex can have profound effects on its resulting anatomy, physiology and behavior. Here we treat intrauterine position as a combinatorial problem and determine the theoretical probability of having 0, 1 or 2 adjacent foetuses of the opposite sex for species with random and biased distribution of genders in uterine horns (mice and gerbils), and where the influence of an \"upstream\" male has been proposed to be a factor (rats). As overall litter size increases the probabilities of having 0, 1, or 2 adjacent foetuses of the opposite sex approaches and eventually settles at 0.25, 0.5, 0.25 respectively. However, at biologically-relevant litter sizes probabilities are more variable and the general effect of an increase in litter size is to increase the probability that any particular foetus will be flanked by two members of the opposite sex. When gender ratios within a uterine horn are no longer balanced, the probability that there are 0 adjacent foetuses of the opposite sex increases.

developmental biology↗

bioRxiv2017

A protein phosphatase network controls temporal and spatial dynamics of differentiation commitment in human epidermis

Epidermal homeostasis depends on a balance between stem cell renewal and terminal differentiation. The transition between the two cell states, termed commitment, is poorly understood. Here we characterise commitment by integrating transcriptomic and proteomic data from disaggregated primary human keratinocytes held in suspension for up to 12h to induce differentiation. We find that cell detachment induces a network of protein phosphatases. The pro-commitment phosphatases - including DUSP6, PPTC7, PTPN1, PTPN13 and PPP3CA - promote differentiation by negatively regulating ERK MAPK and positively regulating AP1 transcription factors. Their activity is antagonised by concomitant upregulation of DUSP10. Boolean network modelling of phosphatase interactions identifies commitment as an inherently unstable biological switch between the stem and differentiated cell states. Furthermore, phosphatase expression is spatially regulated both in vivo and in vitro. We conclude that an auto-regulatory phosphatase network maintains epidermal homeostasis by controlling the onset and duration of commitment.

developmental biology↗

bioRxiv2017

Aubergine And piRNAs Repress The Proto-Oncogene Cbl For Germline Stem Cell Self-Renewal

PIWI proteins have essential roles in germ cells and stem cell lineages. In Drosophila, Piwi is required in somatic niche cells and germline stem cells (GSCs) for GSC self-renewal and differentiation. Whether and how other PIWI proteins are involved in GSC biology remains unknown. Here, we show that Aubergine (Aub), another PIWI protein, is intrinsically required in GSCs for their self-renewal and differentiation. Aub loading with piRNAs is essential for these functions. The major role of Aub is in self-renewal and depends on mRNA regulation. We identify the Cbl proto-oncogene, a regulator of mammalian hematopoietic stem cells, as a novel GSC differentiation factor. Aub represses Cbl mRNA translation for GSC self-renewal, and does so through recruitment of the CCR4-NOT complex. This study reveals the role of piRNAs and PIWI proteins in translational repression for stem cell homeostasis and highlights piRNAs as major post-transcriptional regulators in key developmental decisions.

developmental biology↗