Transgenic quails reveal dynamic TCF/ß-catenin signaling during avian embryonic development.

The Wnt/ß-catenin signaling pathway is highly conserved throughout evolution, playing crucial roles in several developmental and pathological processes. Wnt ligands can act at a considerable distance from their sources and it is therefore necessary to examine not only the Wnt-producing but also the Wnt-receiving cells and tissues to fully appreciate the many functions of this pathway. To monitor Wnt activity, multiple tools have been designed which consist of multimerized Wnt signaling response elements (TCF/LEF binding sites) driving the expression of fluorescent reporter proteins (e.g. GFP, RFP) or of LacZ. The high stability of those reporters leads to a considerable accumulation in cells activating the pathway, thereby making them easily detectable. However, this makes them unsuitable to follow temporal changes of the pathway's activity during dynamic biological events. Even though fluorescent transcriptional reporters can be destabilized to shorten their half-lives, this dramatically reduces signal intensities, particularly when applied in vivo. To alleviate these issues, we developed two transgenic quail lines in which high copy number (12× or 16×) of the TCF/LEF binding sites drive the expression of destabilized GFP variants. Translational enhancer sequences derived from viral mRNAs were used to increase signal intensity and specificity. This resulted in transgenic lines efficient for the characterization of TCF/ß-catenin transcriptional dynamic activities during embryogenesis, including using in vivo imaging. Our analyses demonstrate the use of this transcriptional reporter to unveil novel aspects of Wnt signaling, thus opening new routes of investigation into the role of this pathway during amniote embryonic development.

TGFß signalling acts as a molecular brake of myoblast fusion.

Fusion of nascent myoblasts to pre-existing myofibres is critical for skeletal muscle growth and repair. The vast majority of molecules known to regulate myoblast fusion are necessary in this process. Here, we uncover, through high-throughput in vitro assays and in vivo studies in the chicken embryo, that TGFß (SMAD2/3-dependent) signalling acts specifically and uniquely as a molecular brake on muscle fusion. While constitutive activation of the pathway arrests fusion, its inhibition leads to a striking over-fusion phenotype. This dynamic control of TGFß signalling in the embryonic muscle relies on a receptor complementation mechanism, prompted by the merging of myoblasts with myofibres, each carrying one component of the heterodimer receptor complex. The competence of myofibres to fuse is likely restored through endocytic degradation of activated receptors. Altogether, this study shows that muscle fusion relies on TGFß signalling to regulate its pace.

Macrophages provide a transient muscle stem cell niche via NAMPT secretion.

Skeletal muscle regenerates through the activation of resident stem cells. Termed satellite cells, these normally quiescent cells are induced to proliferate by wound-derived signals1. Identifying the source and nature of these cues has been hampered by an inability to visualize the complex cell interactions that occur within the wound. Here we use muscle injury models in zebrafish to systematically capture the interactions between satellite cells and the innate immune system after injury, in real time, throughout the repair process. This analysis revealed that a specific subset of macrophages 'dwell' within the injury, establishing a transient but obligate niche for stem cell proliferation. Single-cell profiling identified proliferative signals that are secreted by dwelling macrophages, which include the cytokine nicotinamide phosphoribosyltransferase (Nampt, which is also known as visfatin or PBEF in humans). Nampt secretion from the macrophage niche is required for muscle regeneration, acting through the C-C motif chemokine receptor type 5 (Ccr5), which is expressed on muscle stem cells. This analysis shows that in addition to their ability to modulate the immune response, specific macrophage populations also provide a transient stem-cell-activating niche, directly supplying proliferation-inducing cues that govern the repair process that is mediated by muscle stem cells. This study demonstrates that macrophage-derived niche signals for muscle stem cells, such as NAMPT, can be applied as new therapeutic modalities for skeletal muscle injury and disease.

Transgenesis and web resources in quail.

Due to its amenability to manipulations, to live observation and its striking similarities to mammals, the chicken embryo has been one of the major animal models in biomedical research. Although it is technically possible to genome-edit the chicken, its long generation time (6 months to sexual maturity) makes it an impractical lab model and has prevented it widespread use in research. The Japanese quail (Coturnix coturnix japonica) is an attractive alternative, very similar to the chicken, but with the decisive asset of a much shorter generation time (1.5 months). In recent years, transgenic quail lines have been described. Most of them were generated using replication-deficient lentiviruses, a technique that presents diverse limitations. Here, we introduce a novel technology to perform transgenesis in quail, based on the in vivo transfection of plasmids in circulating Primordial Germ Cells (PGCs). This technique is simple, efficient and allows using the infinite variety of genome engineering approaches developed in other models. Furthermore, we present a website centralizing quail genomic and technological information to facilitate the design of genome-editing strategies, showcase the past and future transgenic quail lines and foster collaborative work within the avian community.

Chick muscle development.

Striated muscle is the most abundant tissue in the body of vertebrates and it forms, together with the skeleton, the locomotory system required both for movement and the creation of the specific body shape of a species. Research on the embryonic development of muscles has a long tradition both in classical embryology and in molecular developmental biology. While the gene networks regulating muscle development have been discovered mostly in the mouse through genetics, our knowledge on cell lineages, muscle morphogenesis and tissue interactions regulating their formation is to a large extent based on the use of the avian model. This review highlights present knowledge of the development of skeletal muscle in vertebrate embryos. Special focus will be placed on the contributions from chicken and quail embryo model systems.

Phosphorylation of Lbx1 controls lateral myoblast migration into the limb.

The migration of limb myogenic precursors from limb level somites to their ultimate site of differentiation in the limb is a paradigmatic example of a set of dynamic and orchestrated migratory cell behaviours. The homeobox containing transcription factor ladybird homeobox 1 (Lbx1) is a central regulator of limb myoblast migration, null mutations of Lbx1 result in severe disruptions to limb muscle formation, particularly in the distal region of the limb in mice (Gross et al., 2000). As such Lbx1 has been hypothesized to control lateral migration of myoblasts into the distal limb anlage. It acts as a core regulator of the limb myoblast migration machinery, controlled by Pax3. A secondary role for Lbx1 in the differentiation and commitment of limb musculature has also been proposed (Brohmann et al., 2000; Uchiyama et al., 2000). Here we show that lateral migration, but not differentiation or commitment of limb myoblasts, is controlled by the phosphorylation of three adjacent serine residues of LBX1. Electroporation of limb level somites in the chick embryo with a dephosphomimetic form of Lbx1 results in a specific defect in the lateral migration of limb myoblasts. Although the initial delamination and migration of myoblasts is unaffected, migration into the distal limb bud is severely disrupted. Interestingly, myoblasts undergo normal differentiation independent of their migratory status, suggesting that the differentiation potential of hypaxial muscle is not regulated by the phosphorylation state of LBX1. Furthermore, we show that FGF8 and ERK mediated signal transduction, both critical regulators of the developing limb bud, have the capacity to induce the phosphorylation of LBX1 at these residues. Overall, this suggests a mechanism whereby the phosphorylation of LBX1, potentially through FGF8 and ERK signalling, controls the lateral migration of myoblasts into the distal limb bud.

CRISPR/Cas9 in the Chicken Embryo.

Genome editing is driving a revolution in the biomedical sciences that carries the promise for future treatments of genetic diseases. The CRISPR/Cas9 system of RNA-guided genome editing has been successfully applied to modify the genome of a wide spectrum of organisms. We recently showed that this technique can be combined with in vivo electroporation to inhibit the function of genes of interest in somatic cells of the developing chicken embryo. We present here a simplified version of the previously described technique that leads to effective gene loss-of-function.

The chicken embryo as an efficient model to test the function of muscle fusion genes in amniotes.

The fusion of myoblasts into multinucleated myotubes is a crucial step of muscle growth during development and of muscle repair in the adult. While multiple genes were shown to play a role in this process, a vertebrate model where novel candidates can be tested and analyzed at high throughput and relative ease has been lacking. Here, we show that the early chicken embryo is a fast and robust model in which functional testing of muscle fusion candidate genes can be performed. We have used known modulators of muscle fusion, Rac1 and Cdc42, along with the in vivo electroporation of integrated, inducible vectors, to show that the chicken embryo is a suitable model in which their function can be tested and quantified. In addition to nuclei content, specific characteristics of the experimental model allow a fine characterization of additional morphological features that are nearly impossible to assess in other model organisms. This study should establish the chicken embryo as a cheap, reliable and powerful model in which novel vertebrate muscle fusion candidates can be evaluated.

Cytoplasmic NOTCH and membrane-derived ß-catenin link cell fate choice to epithelial-mesenchymal transition during myogenesis.

How cells in the embryo coordinate epithelial plasticity with cell fate decision in a fast changing cellular environment is largely unknown. In chick embryos, skeletal muscle formation is initiated by migrating Delta1-expressing neural crest cells that trigger NOTCH signaling and myogenesis in selected epithelial somite progenitor cells, which rapidly translocate into the nascent muscle to differentiate. Here, we uncovered at the heart of this response a signaling module encompassing NOTCH, GSK-3ß, SNAI1 and ß-catenin. Independent of its transcriptional function, NOTCH profoundly inhibits GSK-3ß activity. As a result SNAI1 is stabilized, triggering an epithelial to mesenchymal transition. This allows the recruitment of ß-catenin from the membrane, which acts as a transcriptional co-factor to activate myogenesis, independently of WNT ligand. Our results intimately associate the initiation of myogenesis to a change in cell adhesion and may reveal a general principle for coupling cell fate changes to EMT in many developmental and pathological processes.

CRISPR mediated somatic cell genome engineering in the chicken.

Gene-targeted knockout technologies are invaluable tools for understanding the functions of genes in vivo. CRISPR/Cas9 system of RNA-guided genome editing is revolutionizing genetics research in a wide spectrum of organisms. Here, we combined CRISPR with in vivo electroporation in the chicken embryo to efficiently target the transcription factor PAX7 in tissues of the developing embryo. This approach generated mosaic genetic mutations within a wild-type cellular background. This series of proof-of-principle experiments indicate that in vivo CRISPR-mediated cell genome engineering is an effective method to achieve gene loss-of-function in the tissues of the chicken embryo and it completes the growing genetic toolbox to study the molecular mechanisms regulating development in this important animal model.

The avian embryo as a model system for skeletal myogenesis.

This review will focus on the use of the chicken and quail as model systems to analyze myogenesis and as such will emphasize the experimental approaches that are strongest in these systems-the amenability of the avian embryo to manipulation and in ovo observation. During somite differentiation, a wide spectrum of developmental processes occur such as cellular differentiation, migration, and fusion. Cell lineage studies combined with recent advancements in cell imaging allow these biological phenomena to be readily observed and hypotheses tested extremely rapidly-a strength that is restricted to the avian system. A clear weakness of the chicken in the past has been genetic approaches to modulate gene function. Recent advances in the electroporation of expression vectors, siRNA constructs, and use of tissue specific reporters have opened the door to increasingly sophisticated experiments that address questions of interest not only to the somite/muscle field in particular but also fundamental to biology in general. Importantly, an ever-growing body of evidence indicates that somite differentiation in birds is indistinguishable to that of mammals; therefore, these avian studies complement the complex genetic models of the mouse.

A dynamic analysis of muscle fusion in the chick embryo.

Skeletal muscle development, growth and regeneration depend upon the ability of muscle cells to fuse into multinucleated fibers. Surprisingly little is known about the cellular events that underlie fusion during amniote development. Here, we have developed novel molecular tools to characterize muscle cell fusion during chick embryo development. We show that all cell populations arising from somites fuse, but each with unique characteristics. Fusion in the trunk is slow and independent of fiber length. By contrast, the addition of nuclei in limb muscles is three times more rapid than in trunk and is tightly associated with fiber growth. A complex interaction takes place in the trunk, where primary myotome cells from the medial somite border rarely fuse to one another, but readily do so with anterior and posterior border cells. Conversely, resident muscle progenitors actively fuse with one another, but poorly with the primary myotome. In summary, this study unveils an unexpected variety of fusion behaviors in distinct embryonic domains that is likely to reflect a tight molecular control of muscle fusion in vertebrates.

Migrating cells mediate long-range WNT signaling.

In amniotes, it is widely accepted that WNTs secreted by the dorsal neural tube form a concentration gradient that regulates early somite patterning and myotome organization. Here we demonstrate in the chicken embryo that WNT protein is not secreted to act at a distance, but rather loaded onto migrating neural crest cells that deliver it to somites. Inhibiting neural crest migration or ablating their population has a profound impact on the WNT response in somites. Furthermore, we show that a central player in the efficient delivery of WNT to somites is the heparan sulfate proteoglycan GPC4, expressed by neural crest. Together, our data describe a novel mode of signaling whereby WNT proteins hitch a ride on migratory neural crest cells to pattern the somites at a distance from its source.

ErbB3 binding protein-1 (Ebp1) controls proliferation and myogenic differentiation of muscle stem cells.

Satellite cells are resident stem cells of skeletal muscle, supplying myoblasts for post-natal muscle growth, hypertrophy and repair. Many regulatory networks control satellite cell function, which includes EGF signalling via the ErbB family of receptors. Here we investigated the role of ErbB3 binding protein-1 (Ebp1) in regulation of myogenic stem cell proliferation and differentiation. Ebp1 is a well-conserved DNA/RNA binding protein that is implicated in cell growth, apoptosis and differentiation in many cell types. Of the two main Ebp1 isoforms, only p48 was expressed in satellite cells and C2C12 myoblasts. Although not present in quiescent satellite cells, p48 was strongly induced during activation, remaining at high levels during proliferation and differentiation. While retroviral-mediated over-expression of Ebp1 had only minor effects, siRNA-mediated Ebp1 knockdown inhibited both proliferation and differentiation of satellite cells and C2C12 myoblasts, with a clear failure of myotube formation. Ebp1-knockdown significantly reduced ErbB3 receptor levels, yet over-expression of ErbB3 in Ebp1 knockdown cells did not rescue differentiation. Ebp1 was also expressed by muscle cells during developmental myogenesis in mouse. Since Ebp1 is well-conserved between mouse and chick, we switched to chick to examine its role in muscle formation. In chick embryo, Ebp1 was expressed in the dermomyotome, and myogenic differentiation of muscle progenitors was inhibited by specific Ebp1 down-regulation using shRNA electroporation. These observations demonstrate a conserved function of Ebp1 in the regulation of embryonic muscle progenitors and adult muscle stem cells, which likely operates independently of ErbB3 signaling.

Long-term, inducible gene loss-of-function in the chicken embryo.

The use of shRNAmir to down-regulate the expression of genes of interest is a powerful tool for studying gene function during early chick development. However, because of the limitations of electroporation-mediated transgenesis, the down-regulation of genes expressed at late stages of development in specific tissues is difficult to perform. By combining electroporation of a doxycycline-inducible, miR30-based shRNA plasmid with the Tol2 genomic integration system, we are now able to down-regulate the expression of any gene of interest at defined stage of chicken development.

Two distinct muscle progenitor populations coexist throughout amniote development.

During embryonic and fetal life, skeletal muscle growth is dependent upon the proliferation and the differentiation of a population of resident muscle progenitors, from which derive the muscle stem cells of the adult, the satellite cells. Under poorly defined extrinsic and intrinsic influences, muscle progenitors proliferate, differentiate or enter a quiescent state to become reserve satellite cells. Despite their primordial role, surprisingly little is known on the homeostasis of resident progenitors during embryogenesis. Preliminary studies in chick and mouse describing the key progenitor populations contributing to muscle growth during embryogenesis have led to differing results that could be due to technical issues or to fundamental differences between animal models. To address this question, we have undertaken a comprehensive analysis of the state of differentiation and proliferation of muscle progenitor cells from the time of their emergence within the dermomyotome until late fetal life, when they adopt a satellite cell-like position under the basal lamina. This was done by immunostaining against key players of myogenic differentiation, in muscles chosen from different regions of the body in two model organisms, the chick and mouse. This study identified two co-existing populations of progenitors during embryonic and fetal life in both chick and mouse: a minor, slow-cycling pool of undifferentiated resident progenitors which express Pax7, co-existing with a major fast-cycling population that co-express Pax7 and the early myogenic differentiation marker Myf5. We found that the overall proliferation rate of both progenitors drastically decreased with embryonic age, as an increasingly large portion of slow and fast-cycling progenitors entered quiescence during development. Together, this data suggests that the cellular strategies that drive muscle growth during embryonic and fetal life are remarkably conserved in amniotes throughout evolution. They rely on the tight regulation of proliferation, entry in quiescence, and modulation of the cell cycle's length for both of the co-existing populations of muscle progenitors to maintain the homeostasis of growing muscles during development.

The Zebrafish Anatomy Portal: a novel integrated resource to facilitate zebrafish research.

Zebrafish is a common model organism in research and yet, despite its widespread use, anatomical resources for this species are incomplete or lacking in functionality. There remains a need for a single reference resource that integrates user-friendly tools to facilitate the identification of structures, display of reference images, provides data on gene expression, links to relevant literature, and covers the complete range of zebrafish developmental stages. To fulfill this need, we have designed the Zebrafish Anatomy Portal (www.zfap.org), containing annotated three-dimensional images of zebrafish at stages throughout development and adulthood, acquired by optical projection tomography. ZFAP combines functionalities to allow scanning through 3D data sets, searching of images by anatomical terms, predictions of gene expression from literature analysis, and facilitation of the identification of relevant literature through assisted searching of the NCBI PubMed resource. ZFAP provides a highly functional anatomical resource that will aid future education and research in the zebrafish model system.

MyMiner: a web application for computer-assisted biocuration and text annotation.

MOTIVATION: The exponential growth of scientific literature has resulted in a massive amount of unstructured natural language data that cannot be directly handled by means of bioinformatics tools. Such tools generally require structured data, often generated through a cumbersome process of manual literature curation. Herein, we present MyMiner, a free and user-friendly text annotation tool aimed to assist in carrying out the main biocuration tasks and to provide labelled data for the development of text mining systems. MyMiner allows easy classification and labelling of textual data according to user-specified classes as well as predefined biological entities. The usefulness and efficiency of this application have been tested for a range of real-life annotation scenarios of various research topics. AVAILABILITY: http://myminer.armi.monash.edu.au.

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.

There is an increasing interest in developing ontologies and controlled vocabularies to improve the efficiency and consistency of manual literature curation, to enable more formal biocuration workflow results and ultimately to improve analysis of biological data. Two ontologies that have been successfully used for this purpose are the Gene Ontology (GO) for annotating aspects of gene products and the Molecular Interaction ontology (PSI-MI) used by databases that archive protein-protein interactions. The examination of protein interactions has proven to be extremely promising for the understanding of cellular processes. Manual mapping of information from the biomedical literature to bio-ontology terms is one of the most challenging components in the curation pipeline. It requires that expert curators interpret the natural language descriptions contained in articles and infer their semantic equivalents in the ontology (controlled vocabulary). Since manual curation is a time-consuming process, there is strong motivation to implement text-mining techniques to automatically extract annotations from free text. A range of text mining strategies has been devised to assist in the automated extraction of biological data. These strategies either recognize technical terms used recurrently in the literature and propose them as candidates for inclusion in ontologies, or retrieve passages that serve as evidential support for annotating an ontology term, e.g. from the PSI-MI or GO controlled vocabularies. Here, we provide a general overview of current text-mining methods to automatically extract annotations of GO and PSI-MI ontology terms in the context of the BioCreative (Critical Assessment of Information Extraction Systems in Biology) challenge. Special emphasis is given to protein-protein interaction data and PSI-MI terms referring to interaction detection methods.