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bioRxiv2019

The Prrx1 limb enhancer marks an adult population of injury-responsive, multipotent dermal fibroblasts

The heterogeneity of adult tissues has been posited to contribute toward the loss of regenerative potential in mammals. Here we characterize an adult population of dermal fibroblasts that maintain expression of a Prrx1 enhancer which originally marked mesenchymal limb progenitors. Prrx1 enhancer-positive cells (Prrx1enh+) make up a small subset of adult dermal cells (~0.2%) and reside mainly within specific dermal perivascular and hair follicle niches. Upon injury, however, Prrx1enh+ cells readily migrate into the wound bed and amplify on average 16-fold beyond their uninjured numbers. Additionally, Prrx1enh+ cells emigrate out of their dermal niches following wounding and contribute to subcutaneous tissue. Prrx1enh+ cells are uniquely injury-responsive and do not contribute to tissue homeostasis or enriched by neonatal-like Wnt signaling. Prrx1enh+ cells represent a potent regenerative cell population that, despite being a meager minority in adult skin, demonstrate the potential to tip the balance of mammalian wound healing toward scar-free healing.

developmental biology↗

bioRxiv2019

SWI/SNF component BAF250a coordinates OCT4 and WNT signaling pathway to control cardiac lineage differentiation

Dissecting epigenetic mechanisms controlling early cardiac differentiation will provide insights into heart regeneration and heart disease treatment. SWI/SNF complexes remodel nucleosomes to regulate gene expression and play a key role in organogenesis. Here we reported a unique function of BAF250a in regulating the physical interaction of OCT4 and {beta}-CATENIN during cardiac lineage differentiation from human ESCs. BAF250a deletion greatly reduced the physical interaction between OCT4 and {beta}-CATENIN but did not alter the expression of {beta}-CATENIN and OCT4 in the mesodermal progenitor cells. BAF250a ablation led to decreased recruitment of OCT4 and {beta}-CATENIN at promoters of key mesodermal lineage genes, such as MESP1 and EOMES. Subsequently, the expression of lineage specific genes was down-regulated whereas the expression of pluripotent genes was up-regulated. In parallel, BAF250a ablation also altered recruitments of OCT4 and {beta}-CATENIN to the promoter of CCND2 and CCND3, two key genes for S phase entry during cell cycle. Consequently, BAF250a deletion led to prolonged S phase in Mesp1+ cardiac progenitor cells, which in turn inhibited efficient differentiation of Mesp1+ to Isl1+ cells. Furthermore, BAF250a deletion abolished the interaction of OCT4 and BRG1 in mesoderm, suggesting that BAF250a is the key component in SWI/SNF complex that determines the interaction of Oct4/{beta}-catenin in mesoderm. In contrast, we found that BAF250a did not regulate the OCT4/{beta}-CATENIN interaction during neuroectoderm differentiation. Altogether, our results suggest that BAF250a specifically controls proper cardiac mesoderm differentiation by reorganizing the binding of OCT4/{beta}-CATENIN and regulates both key lineage differentiation genes and cell cycle genes coincided in response to WNT/{beta}-CATENIN signal.\n\nHighlightsBAF250a is required for hESC cardiac differentiation\n\nBAF250a is required for the assembly of Brg1/OCT4/{beta}-CATENIN complex and the recruitment of OCT4/{beta}-CATENIN to cardiac genes\n\nBAF250a is dispensable for the interaction of OCT4/{beta}-CATENIN interaction in neuroectoderm differentiation\n\nBAF250a interacts with OCT4/{beta}-CATENIN to promote cardiac differentiation by regulating cell cycle.

developmental biology↗

bioRxiv2019

Tissue nonspecific alkaline phosphatase improves bone quality but does not alleviate craniosynostosis in the FGFR2C342Y/+ mouse model of Crouzon syndrome

Craniosynostosis is the premature fusion of cranial bones. The goal of this study was to determine if delivery of recombinant tissue nonspecific alkaline phosphatase (TNAP) could prevent or diminish the severity of craniosynostosis in a C57BL/6 FGFR2C342Y/+ model of neonatal onset craniosynostosis or a BALB/c FGFR2C342Y/+ model of postnatal onset craniosynostosis. Mice were injected with a lentivirus encoding a mineral targeted form of TNAP immediately after birth. Cranial bone fusion as well as cranial bone volume, mineral content and density were assessed by micro computed tomography. Craniofacial shape was measured with calipers. Alkaline phosphatase, alanine amino transferase (ALT) and aspartate amino transferase (AST) activity levels were measured in serum. Neonatal delivery of TNAP diminished craniosynostosis severity from 94% suture obliteration in vehicle treated mice to 67% suture obliteration in treated mice, p<0.02) and the incidence of malocclusion from 82.4% to 34.7% (p<0.03), with no effect on cranial bone in C57BL/6 FGFR2C342Y/+ mice. In contrast, treatment with TNAP improved cranial bone volume (p< 0.01), density (p< 0.01) and mineral content (p< 0.01) but had no effect on craniosynostosis or malocclusion in BALB/c FGFR2C342Y/+ mice. These results indicate that perinatal recombinant TNAP enzyme therapy diminishes craniosynostosis severity in the C57BL/6 FGFR2C342Y/+ neonatal onset mouse model of Crouzon syndrome, and that effects of exogenous TNAP are genetic background dependent.

developmental biology↗

bioRxiv2019

Krüppel-like factor gene function in the ctenophore Mnemiopsis suggests an ancient role in promoting cell proliferation in metazoan stem cell niches

The Kruppel-like factor (Klf) gene family encodes for transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation, and development in bilaterians. While Klf genes have been shown to functionally specify various cell types in non-bilaterian animals, their role in early diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis results in abnormal development of several organs including the pharynx, tentacle bulbs, and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation. Summary StatementUsing CRISPR/Cas9 genome editing and morpholino oligonucleotide knockdown, this study shows that tissues derived from the endoderm are dependent upon Klf5 ortholog expression for proper development and patterning in the ctenophore Mnemiopsis leidyi.

developmental biology↗

bioRxiv2019

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Circulating endocrine factors are critical for orchestrating complex developmental processes during the generation of adult form. One such factor, thyroid hormone, regulates diverse cellular processes during post-embryonic development and can drive disparate morphological outcomes through mechanisms that remain essentially unknown. We sought to define how thyroid hormone elicits opposite responses in the abundance of two pigment cell classes during development of the zebrafish adult pigment pattern. By profiling individual transcriptomes from thousands of neural crest derived cells, including pigment cells, we reconstructed developmental trajectories and identified lineage-specific changes in response to thyroid hormone. Our findings show that thyroid hormone and its receptors regulate distinct events of cellular maturation across lineages, and illustrate how a single, global factor integrates seemingly divergent morphogenetic outcomes across developmental time.

developmental biology↗

bioRxiv2019

Parallel control of mechanosensory hair cell orientation by the PCP and Wnt pathways

Cell polarity plays a crucial role during development of vertebrates and invertebrates. Planar Cell Polarity (PCP) is defined as the coordinated polarity of cells within a tissue axis and is essential for processes such as gastrulation, neural tube closure or hearing. Wnt ligands can be instructive or permissive during PCP-dependent processes, and Wnt pathway mutants are often classified as PCP mutants due to the complexity and the similarities between their phenotypes. Our studies of the zebrafish sensory lateral line reveal that disruptions of the PCP and Wnt pathways have differential effects on hair cell orientations. While mutations in PCP genes cause random orientations of hair cells, mutations in Wnt pathway members induce hair cells to adopt a concentric pattern. We show that PCP signaling is normal in hair cells of Wnt pathway mutants and that the concentric hair cell phenotype is due to altered organization of the surrounding support cells. Thus, the PCP and Wnt pathways work in parallel, as separate pathways to establish proper hair cell orientation. Our data suggest that coordinated support cell organization is established during the formation of lateral line primordia, much earlier than the appearance of hair cells. Together, these finding reveal that hair cell orientation defects are not solely explained by defects in PCP signaling and that some hair cell phenotypes warrant reevaluation.

developmental biology↗

bioRxiv2019

N6-methyladenosine dynamics during early vertebrate embryogenesis

Early vertebrate embryogenesis is characterized by extensive post-transcriptional regulation during the maternal-to-zygotic transition. The N6-methyladenosine (m6A) modifications on mRNA have been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with polyadenylated mRNA levels. The majority (>70%) of maternal transcripts harbor m6A, and there is a substantial increase of m6A in the polyadenylated mRNA fraction between 0 and 2 hours post fertilization. Notably, we find strong associations between m6A, cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation (ZGA). Interestingly, the relationship between m6A and translation is strongest for peaks located in the 3UTR, but not overlapping stop codons. Sequence analyses revealed enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. After ZGA, m6A seem to diminish the effect of miR-430 mediated degradation. The reported results improve our understanding of the combinatorial code behind post-transcriptional mRNA regulation during embryonic reprogramming and early differentiation.

developmental biology↗

bioRxiv2019

Piezo1 is required for outflow tract and aortic valve development.

Aims-During embryogenesis, the onset of circulatory blood flow generates a variety of hemodynamic forces which reciprocally induce changes in cardiovascular development and performance. It has been known for some time that these forces can be detected by as yet unknown mechanosensory systems which in turn promote cardiogenic events such as outflow tract and aortic valve development. PIEZO1 is a mechanosensitive ion channel present in endothelial cells where it serves to detect hemodynamic forces making it an ideal candidate to play a role during cardiac development. We sought to determine whether PIEZO1 is required for outflow tract and aortic valve development. Methods and results-By analysing heart development in zebrafish we have determined that piezo1 is expressed in the developing outflow tract where it serves to detect hemodynamic forces. In particular, we have found that mechanical forces generated during the cardiac cycle activate Piezo1 which triggers nitric oxide to be released in the outflow tract. Consequently, disrupting Piezo1 signalling leads to defective outflow tract and aortic valve development and indicates this gene may be involved in the etiology of congenital heart diseases. Based on these findings, we analysed genomic data generated from a cohort of bicuspid aortic valve patients and identified 3 probands who each harboured a novel variant in PIEZO1. Subsequent in vitro and in vivo assays indicates that these variants behave as dominant negatives leading to an inhibition of normal PIEZO1 mechanosensory activity and defective aortic valve development. Conclusion-These data indicate that the mechanosensitive ion channel piezo1 is required for OFT and aortic valve development and, furthermore, dominant negative variants of PIEZO1 appear to be associated with BAV in humans.

developmental biology↗

bioRxiv2019

Life history parameters in acellular extrinsic fiber cementum microstructure

Life-history parameters such as pregnancies, skeletal trauma, and renal disease have previously been identified from hypomineralized growth layers (incremental lines) of acellular extrinsic fiber cementum (AEFC). The precise periodicity of these growth layers remains vaguely approximated, so causal life-history explanations using tooth cementum cannot yet be rigorously calculated or tested. On the other hand, we show how life history parameters in AEFC can be identified by two contrasting elemental detection methods. Based on our results we reject the possibility of accurate estimation of pregnancies and other life history parameters from cementum using scanning electron microscopy alone. Here, we propose a new methodological approach for cementum research, Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), to measure degree and distribution of mineralization of cementum growth layers. Our results show that Tof-SIMS can significantly increase our knowledge of cementum composition and is therefore a powerful new tool for life history researchers.

developmental biology↗

bioRxiv2019

Preformed Chromatin Topology Assists TranscriptionalRobustness of Shh during Limb Development

Long-range gene regulation involves physical proximity between enhancers and promoters to generate precise patterns of gene expression in space and time. However, in some cases proximity coincides with gene activation, whereas in others preformed topologies already exist before activation. In this study, we investigate the preformed configuration underlying the regulation of the Shh gene by its unique limb enhancer, the ZRS, in vivo during mouse development. Abrogating the constitutive transcription covering the ZRS region led to a shift within the Shh-ZRS contacts and a moderate reduction in Shh transcription. Deletion of the CTCF binding sites around the ZRS resulted in a loss of the Shh-ZRS preformed interaction and a 50% decrease in Shh expression but no phenotype, suggesting an additional, CTCF-independent mechanism of promoter-enhancer communication. This residual activity, however, was diminished by combining the loss of CTCF binding with a hypomorphic ZRS allele resulting in severe Shh loss-of-function and digit agenesis. Our results indicate that the preformed chromatin structure of the Shh locus is sustained by multiple components and acts to reinforce enhancer-promoter communication for robust transcription.

developmental biology↗

bioRxiv2019

Mechanically activated Piezo channels control outflow tract valve development through Yap1 and Klf2-Notch signaling axis

Mechanical forces are well known for modulating heart valve developmental programs. Yet, it is still unclear how genetic programs and mechanosensation interact during heart valve development. Here, we assessed the mechanosensitive pathways involved during zebrafish outflow tract (OFT) valve development in vivo. Our results show that the hippo effector Yap1, Klf2, and the Notch signaling pathway are all essential for OFT valve morphogenesis in response to mechanical forces, albeit active in different cell layers. Furthermore, we show that Piezo and TRP mechanosensitive channels are essential for regulating these pathways. In addition, live reporters reveal that piezo controls Klf2 and Notch activity in the endothelium and Yap1 expression in the smooth muscle progenitors to coordinate OFT valve morphogenesis. Together, this work identifies a unique morphogenetic program during OFT valve formation and places Piezo as a central modulator of the cell response to forces in this process.

developmental biology↗

bioRxiv2019

PSMC3 is required for spermatogonia niche establishment in mouse spermatogenesis

Males produce millions of spermatozoa each day, which are originated from spermatogonia. Spermatogonia niche establishment and maintenance and the subsequent haploidization of spermatocytes in meiosis are hallmarks of this process. The function of the individual players and coordinated mechanisms regulating different stages of gametogenesis in mammals are not well understood. In this work we focused on the role of PSMC3 in mouse gametogenesis. We observed that Psmc3 is highly expressed in mouse testis, and it is widely expressed in different stages of gamete formation. Conditional deletion of Psmc3 results in both male and female impairment of gonad development at early pre-meiotic stages, but has no apparent effect on meiosis progression. This is likely a consequence of abnormal spermatogonia niche establishment and/or maintenance, revealed by a massive loss of undifferentiated spermatogonia. Our work defines a fundamental role of PSMC3 functions in spermatogenesis during spermatogonia development with direct implications in fertility.

developmental biology↗

bioRxiv2019

Mutations in thyroid hormone receptor α1 cause premature neurogenesis and progenitor cell depletion in human cortical development

Mutations in the thyroid hormone receptor 1 gene (THRA) have recently been identified as a cause of intellectual deficit in humans. Patients present with structural abnormalities including microcephaly, reduced cerebellar volume and decreased axonal density. Here, we show that directed differentiation of THRA mutant patient-derived iPSCs to forebrain neural progenitors is markedly reduced, but mutant progenitor cells can generate deep and upper cortical layer neurons and form functional neuronal networks. Quantitative lineage tracing shows that THRA mutation-containing progenitor cells exit the cell cycle prematurely, resulting in reduced clonal output. Using a novel micropatterned chip assay, we find that spatial self-organisation of mutation-containing progenitor cells is impaired, consistent with downregulated expression of cell-cell adhesion genes. These results reveal for the first time that thyroid hormone receptor 1 is required for normal neural progenitor cell proliferation and organisation in human cerebral cortical development. They also exemplify novel quantitative approaches for studying neurodevelopmental disorders using patient-derived cells in vitro.

developmental biology↗

bioRxiv2019

Structural redundancy in supracellular actomyosin networks enables robust tissue folding

Tissue morphogenesis is strikingly reproducible. Yet, how tissues are robustly sculpted, even under challenging conditions, is unknown. Here, we combined network analysis, experimental perturbations, and computational modeling to determine how network connectivity between hundreds of contractile cells on the ventral side of the Drosophila embryo ensures robust tissue folding. We identified two network properties that mechanically promote robustness. First, redundant supracellular cytoskeletal network paths ensure global connectivity, even with network degradation. By forming many more connections than are required, morphogenesis is not disrupted by local network damage, analogous to the way redundancy guarantees the large-scale function of vasculature and transportation networks. Second, directional stiffening of edges oriented orthogonal to the folding axis promotes furrow formation at lower contractility levels. Structural redundancy and directional network stiffening ensure robust tissue folding with proper orientation.

developmental biology↗

bioRxiv2019

Defining reprogramming checkpoints from single-cell analysis of induced pluripotency

Elucidating the mechanism of reprogramming is confounded by heterogeneity due to the low efficiency and differential kinetics of obtaining induced pluripotent stem cells (iPSCs) from somatic cells. Therefore, we increased the efficiency with a novel combination of epigenetic and signaling molecules and profiled the transcriptomes of individual reprogramming cells. Contrary to the established temporal order, somatic gene inactivation and upregulation of cell cycle, epithelial, and early pluripotency genes can be triggered independently such that any combination of these events can occur in single cells. Sustained co-expression of Epcam, Nanog, and Sox2 with other genes is required to progress towards iPSCs. Ehf, Phlda2, and translation initiation factor Eif4a1 play novel functional roles in robust iPSC generation. Using regulatory network analysis, we identify a critical role for signaling inhibition by 2i in repressing somatic expression and synergy between the epigenetic modifiers ascorbic acid and a Dot1L inhibitor for pluripotency gene activation.

developmental biology↗

bioRxiv2019

Lineage tracing analysis of cone photoreceptor-associated cis-regulatory elements in the developing chicken retina.

During vertebrate retinal development, transient populations of retinal progenitor cells with restricted cell fate choices are formed. One of these progenitor populations expresses the Thrb gene and can be identified with the ThrbCRM1 cis-regulatory element. Short-term assays have concluded that these cells preferentially generate cone photoreceptors and horizontal cells, however developmental timing has precluded an extensive cell type characterization of their progeny. Here we describe the development and validation of a recombinase-based lineage tracing system for the chicken embryo to further characterize the lineage of these cells. The ThrbCRM1 element was found to preferentially form photoreceptors and horizontal cells, as well as a small number of retinal ganglion cells. The photoreceptor cell progeny are exclusively cone photoreceptors and not rod photoreceptors, confirming that ThrbCRM1-progenitor cells are restricted from the rod fate. In addition, specific subtypes of horizontal cells and retinal ganglion cells were overrepresented, suggesting that ThrbCRM1 progenitor cells are not only restricted for cell type, but for cell subtype as well.

developmental biology↗

bioRxiv2019

Yorkie controls tube length and apical barrier integrity in the developing Drosophila airways

Epithelial organ size and shape depend on cell shape changes, cell-matrix communication and apical membrane growth. The Drosophila embryonic tracheal network is an excellent model to study these processes. Here, we show that the transcriptional co-activator of the Hippo pathway, Yorkie (YAP in vertebrates), plays distinct roles in the developing Drosophila airways. Yorkie exerts a cytoplasmic function by binding Drosophila Twinstar, the orthologue of the vertebrate actin-severing protein Cofilin, to regulate F-actin levels and apical cell membrane size, which are required for proper tracheal tube elongation. Second, Yorkie controls water-tightness of tracheal tubes by transcriptional regulation of the enzyme{delta} -aminolevulinate synthase (Alas). We conclude that Yorkie has a dual role in tracheal development to ensure proper tracheal growth and functionality. Short SummaryThis work identified an alternative role of the transcriptional co-activator Yorkie (Yki) in controlling water impermeability and tube size of the developing Drosophila airways. Tracheal impermeability is triggered by Yki-mediated transcriptional regulation of{delta} -aminolevulinate synthase, Alas, whereas tube elongation is controlled by binding of Yki to the actin severing factor Twinstar.

developmental biology↗

bioRxiv2019

Testing models of mRNA localization reveals robustness regulated by reducing transport between cells

Robust control of gene expression in both space and time is of central importance in the regulation of cellular processes, and for multicellular development. However, the mechanisms by which robustness is achieved are generally not identified or well understood. For example, mRNA localization by molecular-motor-driven transport is crucial for cell polarization in numerous contexts, but the regulatory mechanisms that enable this process to take place in the face of noise or significant perturbations are not fully understood. Here we use a combined experimental-theoretical approach to characterize the robustness of gurken/TGF-alpha mRNA localization in Drosophila egg chambers, where the oocyte and 15 surrounding nurse cells are connected in a stereotypic network via intracellular bridges known as ring canals. We construct a mathematical model that encodes simplified descriptions of the range of steps involved in mRNA localization, including production and transport between and within cells until the final destination in the oocyte. Using Bayesian inference, we calibrate this model using quantitative single molecule fluorescence in situ hybridization data. By analyzing both the steady state and dynamic behaviours of the model, we provide estimates for the rates of different steps of the localization process, as well as the extent of directional bias in transport through the ring canals. The model predicts that mRNA synthesis and transport must be tightly balanced to maintain robustness, a prediction which we tested experimentally using an over-expression mutant. Surprisingly, the over-expression mutant fails to display the anticipated degree of overaccumulation of mRNA in the oocyte predicted by the model. Through careful model-based analysis of quantitative data from the over-expression mutant we show evidence of saturation of transport of mRNA through ring canals. We conclude that this saturation engenders robustness of the localization process, in the face of significant variation in the levels of mRNA synthesis. Statement of significanceFor development to function correctly and reliably across a population, gene expression must be controlled robustly in a repeatable manner. How this robustness is achieved is not well understood. We use modelling to better study the localization of polarity determining transcripts (RNA) in fruit fly development. By calibrating our model with quantitative imaging data we are able to make experimentally testable predictions, comparison of which with data from a genetic mutant, reveals evidence that saturation of RNA transport contributes to the robustness of RNA localization.

developmental biology↗