Threshold-dependent BMP-mediated repression: a model for a conserved mechanism that patterns the neuroectoderm

The epithelial polarity genes frazzled and GUK-holder adjust morphogen gradients to coordinate changes in cell position with cell fate specification

Morphogenetic gradients specify distinct cell populations within tissues. Originally, morphogens were conceived as substances that act on a static field of cells, yet cells usually move during development. Thus, the way cell fates are defined in moving cells remains a significant and largely unsolved problem. Here, we investigated this issue using spatial referencing of cells and 3D spatial statistics in the Drosophila blastoderm to reveal how cell density responds to morphogenetic activity. We show that the morphogen decapentaplegic (DPP) attracts cells towards its peak levels in the dorsal midline, whereas dorsal (DL) stalls them ventrally. We identified frazzled and GUK-holder as the downstream effectors regulated by these morphogens that constrict cells and provide the mechanical force necessary to draw cells dorsally. Surprisingly, GUKH and FRA modulate the DL and DPP gradient levels and this regulation creates a very precise mechanism of coordinating cell movement and fate specification.

The nested embryonic dorsal domains of BMP-target genes are not scaled to size during the evolution of Drosophila species

Egg size is a fast-evolving trait among Drosophilids expected to change the spatial distribution of morphogens that pattern the embryonic axes. Here we asked whether the patterning of the dorsal region of the embryo by the Decapentaplegic/Bone Morphogenetic Protein-4 (DPP/BMP-4) gradient is scaled among Drosophila species with different egg sizes. This region specifies the extra-embryonic tissue amnioserosa and the ectoderm. We find that the entire dorsal region scales with embryo size, but the gene expression patterns regulated by DPP are not proportional, suggesting that the DPP gradient is differentially scaled during evolution. To further test whether the DPP gradient can scale or not in Drosophila melanogaster, we created embryos with expanded dorsal regions that mimic changes in scale seen in other species and measured the resulting domains of DPP-target genes. We find that the proportions of these domains are not maintained, suggesting that the DPP gradient is unable to scale in the embryo. These and previous findings suggest that the embryonic dorso-ventral patterning lack scaling in the ventral and dorsal sides but is robust in the lateral region where the neuroectoderm is specified and two opposing gradients, Dorsal/NFkappa-B and DPP, intersect. We propose that the lack of scaling of the DPP gradient may contribute to changes in the size of the amnioserosa and the numbers of ectodermal cells with specific cortical tensions, which are expected to generate distinct mechanical forces for gastrulating embryos of different sizes.

Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse

Spinal cord development is precisely orchestrated by spatiotemporal gene regulatory programs. However, the underlying epigenetic mechanisms remain largely elusive. Here, we profiled single-cell chromatin accessibility landscapes in mouse neural tubes spanning embryonic days 9.5-13.5. We identified neuronal-cell-cluster-specific cis-regulatory elements in neural progenitors and neurons. Furthermore, we applied a novel computational method, eNet, to build enhancer networks by integrating single-cell chromatin accessibility and gene expression data and identify the hub enhancers within enhancer networks. It was experimentally validated in vivo for Atoh1 that knockout of the hub enhancers, but not the non-hub enhancers, markedly decreased Atoh1 expression and reduced dp1/dI1 cells. Together, our work provides insights into the epigenetic regulation of spinal cord development and a proof-of-concept demonstration of enhancer networks as a general mechanism in transcriptional regulation.

Evolution of the dorsoventral axis in insects: the changing role of Bone Morphogenetic Proteins

Embryonic dorsal-ventral (DV) patterning by Bone Morphogenetic Proteins (BMPs) is a conserved feature of Bilateria, based on graded BMP activity set up by diffusible BMP ligands and Chordin/Sog antagonists. In the fly Drosophila melanogaster BMP function is secondary to patterning by the Toll pathway, suggesting a more restricted role for BMPs in insects. With widespread genome sequencing technologies allied to functional analysis in a growing number of species, recent work has shown that BMP's role in DV patterning relative to Toll varies among insect orders. Further, the role of BMP antagonists to set up BMP gradients is also greatly diversified. Here we review the recent findings concerning the role of BMP in the DV patterning of insects and address the potential aspects that may have co-evolved with BMPs to attain this functional divergence.

Striking parallels between dorsoventral patterning in Drosophila and Gryllus reveal a complex evolutionary history behind a model gene regulatory network

Dorsoventral pattering relies on Toll and BMP signalling in all insects studied so far, with variations in the relative contributions of both pathways. Drosophila and the beetle Tribolium share extensive dependence on Toll, while representatives of more distantly related lineages like the wasp Nasonia and bug Oncopeltus rely more strongly on BMP signalling. Here, we show that in the cricket Gryllus bimaculatus, an evolutionarily distant outgroup, Toll has, like in Drosophila, a direct patterning role for the ventral half of the embryo. In addition, Toll polarises BMP signalling, although this does not involve the conserved BMP inhibitor Sog/Chordin. Finally, Toll activation relies on ovarian patterning mechanisms with striking similarity to Drosophila. Our data suggest two surprising hypotheses: (1) that Toll's patterning function in Gryllus and Drosophila is the result of convergent evolution or (2) a Drosophila-like system arose early in insect evolution and was extensively altered in multiple independent lineages.

A Micropatterned Human-Specific Neuroepithelial Tissue for Modeling Gene and Drug-Induced Neurodevelopmental Defects

The generation of structurally standardized human pluripotent stem cell (hPSC)-derived neural embryonic tissues has the potential to model genetic and environmental mediators of early neurodevelopmental defects. Current neural patterning systems have so far focused on directing cell fate specification spatio-temporally but not morphogenetic processes. Here, the formation of a structurally reproducible and highly-organized neuroepithelium (NE) tissue is directed from hPSCs, which recapitulates morphogenetic cellular processes relevant to early neurulation. These include having a continuous, polarized epithelium and a distinct invagination-like folding, where primitive ectodermal cells undergo E-to-N-cadherin switching and apical constriction as they acquire a NE fate. This is accomplished by spatio-temporal patterning of the mesoendoderm, which guides the development and self-organization of the adjacent primitive ectoderm into the NE. It is uncovered that TGFβ signaling emanating from endodermal cells support tissue folding of the prospective NE. Evaluation of NE tissue structural dysmorphia, which is uniquely achievable in the model, enables the detection of apical constriction and cell adhesion dysfunctions in patient-derived hPSCs as well as differentiating between different classes of neural tube defect-inducing drugs.

Identification of novel Aedes aegypti odorant-binding protein 1 modulators by ligand and structure-based approaches and bioassays

Arboviruses are a group of viruses (e.g. Dengue, Chikungunya and Yellow fever virus) that are transmitted by arthropod vectors, which Aedes aegipty is the vector of main viruses in Americas. This vector is responsible to 2.4 millions of arboviruses cases in Brazil with less than a thousand deaths annually. Despite of epidemiological data, arboviruses treatment is symptomatic and the vaccine control is not effective, which makes the vector control against A. aegipty a promising strategy to diseases control. One way to achieve this goal is to development of A. aegipty sensitive olfactory modulators. Odorant binding protein 1 from A. aegypti (AaegOBP1) is essential in sensory communication, and is the first filter in odorant selection, which makes this target promising to development of new repellents. For this reason, hierarchical virtual screening (ligand-based pharmacophore model and molecular docking) together volatility filter was applied at Sigma-Aldrich database (n = 126.851) to prioritize potential molecules to repellency assays. Three compounds showed adequate stereo-electronic requirements (QFIT> 81.53), score to AaegOBP1 binding site (Score > 36.0) and volatile properties and it was chosen for repellency assays. ZINC00170981 and ZINC00131924 showed a dose-response behavior, while ZINC01621824 did not showed activity in repellency assays. Finally, Molecular Dynamics (MD) was employed to hypothesize the stability of protein-ligand complexes. According to RMSD, RMSF and binding free energy data, ZINC00170981 and ZINC00131924 were able to stabilize AaegOBP1 binding-site during the trajectory by interactions with key residues such as His77, Leu89 and Trp114). Communicated by Ramaswamy H. Sarma.

Coacting enhancers can have complementary functions within gene regulatory networks and promote canalization

Developmental genes are often regulated by multiple enhancers exhibiting similar spatiotemporal outputs, which are generally considered redundantly acting though few have been studied functionally. Using CRISPR-Cas9, we created deletions of two enhancers, brk5' and brk3', that drive similar but not identical expression of the gene brinker (brk) in early Drosophila embryos. Utilizing both in situ hybridization and quantitative mRNA analysis, we investigated the changes in the gene network state caused by the removal of one or both of the early acting enhancers. brk5' deletion generally phenocopied the gene mutant, including expansion of the BMP ligand decapentaplegic (dpp) as well as inducing variability in amnioserosa tissue cell number suggesting a loss of canalization. In contrast, brk3' deletion presented unique phenotypes including dorsal expansion of several ventrally expressed genes and a decrease in amnioserosa cell number. Similarly, deletions were made for two enhancers associated with the gene short-gastrulation (sog), sog.int and sog.dist, demonstrating that they also exhibit distinct patterning phenotypes and affect canalization. In summary, this study shows that similar gene expression driven by coacting enhancers can support distinct, and sometimes complementary, functions within gene regulatory networks and, moreover, that phenotypes associated with individual enhancer deletion mutants can provide insight into new gene functions.

Drosophila Embryonic CNS Development: Neurogenesis, Gliogenesis, Cell Fate, and Differentiation

The Drosophila embryonic central nervous system (CNS) is a complex organ consisting of ∼15,000 neurons and glia that is generated in ∼1 day of development. For the past 40 years, Drosophila developmental neuroscientists have described each step of CNS development in precise molecular genetic detail. This has led to an understanding of how an intricate nervous system emerges from a single cell. These studies have also provided important, new concepts in developmental biology, and provided an essential model for understanding similar processes in other organisms. In this article, the key genes that guide Drosophila CNS development and how they function is reviewed. Features of CNS development covered in this review are neurogenesis, gliogenesis, cell fate specification, and differentiation.

Using Amphioxus as a Basal Chordate Model to Study BMP Signaling Pathway

The BMP signaling pathway has been shown to be involved in different aspects of embryonic development across diverse metazoan phyla. Comparative studies on the roles of the BMP signaling pathway provide crucial insights into the evolution of the animal body plans. In this chapter, we present the general workflow on how to investigate the roles of BMP signaling pathway during amphioxus embryonic development. As amphioxus are basal invertebrate chordates, studies on the BMP signaling pathway in amphioxus could elucidate the functional evolution of BMP pathway in the chordate group. Here, we describe methods for animal husbandry, spawning induction, and manipulation of the BMP signaling pathway during embryonic development through drug inhibitors and recombinant proteins. We also introduce an efficient method of using mesh baskets to handle amphioxus embryos for fluorescence immunostaining and multicolor fluorescence in situ hybridization and to assay the effects of manipulating BMP signaling pathway during amphioxus embryogenesis.

Understanding Pattern Formation in Embryos: Experiment, Theory, and Simulation

Twenty-five years ago, Lewis Wolpert, the eminent developmental biologist, asked the question, "Do We Understand Development?" He concluded that such rapid progress had been made in the preceding two decades that "It is not unreasonable to think that enough will eventually be known to program a computer and simulate some aspects of development." This prediction has been fulfilled, at least partially, with data-driven simulations of several different developmental processes being developed in the intervening years. Nevertheless, the question remains of whether we "understand" development and if simulations are sufficient to provide an explanation of development. While in silico replications and models are undoubtedly an important tool in the investigation and dissection of developmental processes, which complement traditional experimental methods, these need to be supplemented by theory that identifies principles and provides coherent explanations. Here, I use the example of pattern formation in the vertebrate neural tube to illustrate this idea.

N-linked glycosylation restricts the function of Short gastrulation to bind and shuttle BMPs

Disorders of N-linked glycosylation are increasingly reported in the literature. However, the targets that are responsible for the associated developmental and physiological defects are largely unknown. Bone morphogenetic proteins (BMPs) act as highly dynamic complexes to regulate several functions during development. The range and strength of BMP activity depend on interactions with glycosylated protein complexes in the extracellular milieu. Here, we investigate the role of glycosylation for the function of the conserved extracellular BMP antagonist Short gastrulation (Sog). We identify conserved N-glycosylated sites and describe the effect of mutating these residues on BMP pathway activity in Drosophila Functional analysis reveals that loss of individual Sog glycosylation sites enhances BMP antagonism and/or increases the spatial range of Sog effects in the tissue. Mechanistically, we provide evidence that N-terminal and stem glycosylation controls extracellular Sog levels and distribution. The identification of similar residues in vertebrate Chordin proteins suggests that N-glycosylation may be an evolutionarily conserved process that adds complexity to the regulation of BMP activity.

On the origin of leeches by evolution of development

Leeches are a unique group of annelids arising from an ancestor that would be characterized as a freshwater oligochaete worm. Comparative biology of the oligochaetes and the leeches reveals that body plan changes in the oligochaete-to-leech transition probably occurred by addition or modification of the terminal steps in embryonic development and that they were likely driven by a change in the feeding behavior in the ancestor of leeches. In this review article, developmental changes that are associated with the evolution of several leech-specific traits are discussed. These include (1) the evolution of suckers, (2) the loss of chaetae, (3) the loss of septa, and (4) a fixed number of segments. An altered developmental fate of the teloblast is further proposed to be a key factor contributing to the fixation of the segment number, and the evolutionary change in teloblast development may also account for the loss of the ability to regenerate the lost body segments in the leech.

Genetic regulation and function of epidermal growth factor receptor signalling in patterning of the embryonic Drosophila brain

The specification of distinct neural cell types in central nervous system development crucially depends on positional cues conferred to neural stem cells in the neuroectoderm. Here, we investigate the regulation and function of the epidermal growth factor receptor (EGFR) signalling pathway in early development of the Drosophila brain. We find that localized EGFR signalling in the brain neuroectoderm relies on a neuromere-specific deployment of activating (Spitz, Vein) and inhibiting (Argos) ligands. Activated EGFR controls the spatially restricted expression of all dorsoventral (DV) patterning genes in a gene- and neuromere-specific manner. Further, we reveal a novel role of DV genes—ventral nervous system defective (vnd), intermediate neuroblast defective (ind), Nkx6—in regulating the expression of vein and argos, which feed back on EGFR, indicating that EGFR signalling stands not strictly atop the DV patterning genes. Within this network of genetic interactions, Vnd acts as a positive EGFR feedback regulator. Further, we show that EGFR signalling becomes dependent on single-minded-expressing midline cells in the posterior brain (tritocerebrum), but remains midline-independent in the anterior brain (deuto- and protocerebrum). Finally, we demonstrate that activated EGFR controls the proper formation of brain neuroblasts by regulating the number, survival and proneural gene expression of neuroectodermal progenitor cells. These data demonstrate that EGFR signalling is crucially important for patterning and early neurogenesis of the brain.

On the evolution of bilaterality

Bilaterality – the possession of two orthogonal body axes – is the name-giving trait of all bilaterian animals. These body axes are established during early embryogenesis and serve as a three-dimensional coordinate system that provides crucial spatial cues for developing cells, tissues, organs and appendages. The emergence of bilaterality was a major evolutionary transition, as it allowed animals to evolve more complex body plans. Therefore, how bilaterality evolved and whether it evolved once or several times independently is a fundamental issue in evolutionary developmental biology. Recent findings from non-bilaterian animals, in particular from Cnidaria, the sister group to Bilateria, have shed new light into the evolutionary origin of bilaterality. Here, we compare the molecular control of body axes in radially and bilaterally symmetric cnidarians and bilaterians, identify the minimal set of traits common for Bilateria, and evaluate whether bilaterality arose once or more than once during evolution.

Decoding of position in the developing neural tube from antiparallel morphogen gradients

Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation.

Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo

The BMP signaling pathway has a conserved role in dorsal-ventral axis patterning during embryonic development. In Drosophila, graded BMP signaling is transduced by the Mad transcription factor and opposed by the Brinker repressor. In this study, using the Drosophila embryo as a model, we combine RNA-seq with Mad and Brinker ChIP-seq to decipher the BMP-responsive transcriptional network underpinning differentiation of the dorsal ectoderm during dorsal-ventral axis patterning. We identify multiple new BMP target genes, including positive and negative regulators of EGF signaling. Manipulation of EGF signaling levels by loss- and gain-of-function studies reveals that EGF signaling negatively regulates embryonic BMP-responsive transcription. Therefore, the BMP gene network has a self-regulating property in that it establishes a balance between its activity and that of the antagonistic EGF signaling pathway to facilitate correct patterning. In terms of BMP-dependent transcription, we identify key roles for the Zelda and Zerknüllt transcription factors in establishing the resulting expression domain, and find widespread binding of insulator proteins to the Mad and Brinker-bound genomic regions. Analysis of embryos lacking the BEAF-32 insulator protein shows reduced transcription of a peak BMP target gene and a reduction in the number of amnioserosa cells, the fate specified by peak BMP signaling. We incorporate our findings into a model for Mad-dependent activation, and discuss its relevance to BMP signal interpretation in vertebrates.

Embryogenesis involves the patterning of many different cell fates by a limited number of types of signals. One way that these signals promote a particular cell fate is through the induction of a complex, yet highly reproducible, gene expression programme that instructs changes in the cell. For example, there is a conserved role for BMP signals in specifying cell fates during dorsal-ventral axis patterning. Here, we have used genomics approaches to identify the gene expression programme implemented in response to BMP signaling during axis patterning in the Drosophila embryo. Part of the gene network downstream of BMP signaling includes members of the EGF signaling pathway, with our data highlighting reciprocal interactions between these two pathways. We have also determined genome-wide binding of BMP-responsive transcription factors to gain new insights into how the BMP gene network is activated. Our data reveal roles for specific transcription factors and insulator binding proteins, with the latter traditionally associated with the separation of transcriptional domains. Overall, our data will provide a platform for exploiting the tractability of the Drosophila embryo to determine which features of the network are critical drivers of BMP-induced cell fate changes during embryogenesis.

Nervous system development in cephalopods: How egg yolk-richness modifies the topology of the mediolateral patterning system

Cephalopods possess the most complex centralized nervous system among molluscs and the molecular determinants of its development have only begun to be explored. To better understand how evolved their brain and body axes, we studied Sepia officinalis embryos and investigated the expression patterns of neural regionalization genes involved in the mediolateral patterning of the neuroectoderm in model species. SoxB1 expression reveals that the embryonic neuroectoderm is made of several distinct territories that constitute a large part of the animal pole disc. Concentric nkx2.1, pax6/gsx, and pax3/7/msx/pax2/5/8 positive domains subdivide this neuroectoderm. Looking from dorsal to ventral sides, the sequence of these expressions is reminiscent of the mediolateral subdivision in model species, which provides good evidence for "mediolateral patterning" conservation in cephalopods. A specific feature of cephalopod development, however, includes an unconventional orientation to this mediolateral sequence: median markers (like nkx2.1) are unexpectedly expressed at the periphery of the cuttlefish embryo and lateral markers (like Pax3/7) are expressed centrally. As the egg is rich with yolk, the lips of the blastopore (that classically organizes the neural midline) remain unclosed at the lateral side of the animal pole until late stages of organogenesis, therefore reversing the whole embryo topology. These findings confirm - by means of molecular tools - the location of both ventral and dorsal poles in cephalopod embryos.

Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster

We observed heteroses for body weight in Drosophila melanogaster after generating hybrids from three inbred lines. To better understand the mechanism for this phenomenon at the mRNA level, we compared the mRNA profiles of the parental and hybrid lines using high-throughput RNA-seq. A total of 5877 differentially expressed genes (DEGs) were found and about 92% of these exhibited parental expression level dominance. Genes in the dominance category were functionally characterized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the gene classifications offered by the Gene Ontology (GO) Consortium. The analysis identified genes associated with crucial processes such as development and growth in all three crosses. Functional assignments involving aminoglycan metabolism, starch and sucrose metabolism, and galactose metabolism are significantly overrepresented amongst the 215 common dominance DEGs. We conclude that dominance DEGs are important in heteroses in Drosophila melanogaster and contribute specifically to body weight heterosis.

Morphogen rules: design principles of gradient-mediated embryo patterning

The Drosophila blastoderm and the vertebrate neural tube are archetypal examples of morphogen-patterned tissues that create precise spatial patterns of different cell types. In both tissues, pattern formation is dependent on molecular gradients that emanate from opposite poles. Despite distinct evolutionary origins and differences in time scales, cell biology and molecular players, both tissues exhibit striking similarities in the regulatory systems that establish gene expression patterns that foreshadow the arrangement of cell types. First, signaling gradients establish initial conditions that polarize the tissue, but there is no strict correspondence between specific morphogen thresholds and boundary positions. Second, gradients initiate transcriptional networks that integrate broadly distributed activators and localized repressors to generate patterns of gene expression. Third, the correct positioning of boundaries depends on the temporal and spatial dynamics of the transcriptional networks. These similarities reveal design principles that are likely to be broadly applicable to morphogen-patterned tissues.

A trans-Regulatory Code for the Forebrain Expression of Six3.2 in the Medaka Fish

A well integrated and hierarchically organized gene regulatory network is responsible for the progressive specification of the forebrain. The transcription factor Six3 is one of the central components of this network. As such, Six3 regulates several components of the network, but its upstream regulators are still poorly characterized. Here we have systematically identified such regulators, taking advantage of the detailed functional characterization of the regulatory region of the medaka fish Six3.2 ortholog and of a time/cost-effective trans-regulatory screening, which complemented and overcame the limitations of in silico prediction approaches. The candidates resulting from this search were validated with dose-response luciferase assays and expression pattern criteria. Reconfirmed candidates with a matching expression pattern were also tested with chromatin immunoprecipitation and functional studies. Our results confirm the previously proposed direct regulation of Pax6 and further demonstrate that Msx2 and Pbx1 are bona fide direct regulators of early Six3.2 distribution in distinct domains of the medaka fish forebrain. They also point to other transcription factors, including Tcf3, as additional regulators of different spatial-temporal domains of Six3.2 expression. The activity of these regulators is discussed in the context of the gene regulatory network proposed for the specification of the forebrain.

Su(H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryos

In Drosophila embryos, a nuclear gradient of the Dorsal (Dl) transcription factor directs differential gene expression along the dorsoventral (DV) axis, translating it into distinct domains that specify future mesodermal, neural, and ectodermal territories. However, the mechanisms used to differentially position gene expression boundaries along this axis are not fully understood. Here, using a combination of approaches, including mutant phenotype analyses and chromatin immunoprecipitation, we show that the transcription factor Suppressor of Hairless, Su(H), helps define dorsal boundaries for many genes expressed along the DV axis. Synthetic reporter constructs also provide molecular evidence that Su(H) binding sites support repression and act to counterbalance activation through Dl and the ubiquitous activator Zelda. Our study highlights a role for broadly expressed repressors, like Su(H), and organization of transcription factor binding sites within cis-regulatory modules as important elements controlling spatial domains of gene expression to facilitate flexible positioning of boundaries across the entire DV axis.

Sequential actions of β-catenin and Bmp pattern the oral nerve net in Nematostella vectensis

Animal evolution is closely linked to the emergence of the nervous system. At present it is unknown how the basic mechanisms of neural induction and formation of central nervous systems evolved. We addressed this question in Nematostella vectensis, a member of cnidarians, the ancient sister group of bilaterians. We found that β-catenin signalling is crucial for the early induction of the embryonic nervous system. β-Catenin activity at the blastopore induces specific neurogenic genes required for development of the oral nervous system. β-Catenin signalling induces also Bmp signalling, which, at later larval stages, becomes indispensible for the maintenance and asymmetric patterning of the oral nervous system along the primary and secondary (directive) axes. We hypothesize that the consecutive and functionally linked involvement of β-catenin and Bmp signalling in the formation of the cnidarian oral nervous system reflects an ancestral mechanism that evolved before the cnidarian/bilaterian split.

The bilaterian central nervous system is thought to have evolved from a cnidarian-like ancestor, but the mechanisms of neural induction in cnidarians are largely unknown. Here the authors study the cnidarian Nematostella vectensis and show that β-catenin signalling is crucial for the early induction of its embryonic nervous system, suggesting evolutionary roots for this pathway.

Dorsoventral polarity of the Nasonia embryo primarily relies on a BMP gradient formed without input from Toll

In Drosophila, Toll signaling leads to a gradient of nuclear uptake of Dorsal with a peak at the ventral egg pole and is the source for dorsoventral (DV) patterning and polarity of the embryo. In contrast, Toll signaling plays no role in embryonic patterning in most animals, while BMP signaling plays the major role. In order to understand the origin of the novelty of the Drosophila system, we have examined DV patterning in Nasonia vitripennis (Nv), a representative of the Hymenoptera and thus the most ancient branch points within the Holometabola. We have previously shown that while the expression of several conserved DV patterning genes is almost identical in Nasonia and Drosophila embryos at the onset of gastrulation, the ways these patterns evolve in early embryogenesis are very different from what is seen in Drosophila or the beetle Tribolium. In contrast to Drosophila or Tribolium, we find that wasp Toll has a very limited ventral role, whereas BMP is required for almost all DV polarity of the embryo, and these two signaling systems act independently of each other to generate DV polarity. This result gives insights into how the Toll pathway could have usurped a BMP-based DV patterning system in insects. In addition, our work strongly suggests that a novel system for BMP activity gradient formation must be employed in the wasp, since orthologs of crucial components of the fly system are either missing entirely or lack function in the embryo.

BMPs regulate msx gene expression in the dorsal neuroectoderm of Drosophila and vertebrates by distinct mechanisms

In a broad variety of bilaterian species the trunk central nervous system (CNS) derives from three primary rows of neuroblasts. The fates of these neural progenitor cells are determined in part by three conserved transcription factors: vnd/nkx2.2, ind/gsh and msh/msx in Drosophila melanogaster/vertebrates, which are expressed in corresponding non-overlapping patterns along the dorsal-ventral axis. While this conserved suite of “neural identity” gene expression strongly suggests a common ancestral origin for the patterning systems, it is unclear whether the original regulatory mechanisms establishing these patterns have been similarly conserved during evolution. In Drosophila, genetic evidence suggests that Bone Morphogenetic Proteins (BMPs) act in a dosage-dependent fashion to repress expression of neural identity genes. BMPs also play a dose-dependent role in patterning the dorsal and lateral regions of the vertebrate CNS, however, the mechanism by which they achieve such patterning has not yet been clearly established. In this report, we examine the mechanisms by which BMPs act on cis-regulatory modules (CRMs) that control localized expression of the Drosophila msh and zebrafish (Danio rerio) msxB in the dorsal central nervous system (CNS). Our analysis suggests that BMPs act differently in these organisms to regulate similar patterns of gene expression in the neuroectoderm: repressing msh expression in Drosophila, while activating msxB expression in the zebrafish. These findings suggest that the mechanisms by which the BMP gradient patterns the dorsal neuroectoderm have reversed since the divergence of these two ancient lineages.

The trunk nervous system of both vertebrates and invertebrates develops from three primary rows of neural stem cells whose fate is determined by neural identity genes expressed in an evolutionarily conserved dorso-ventral pattern. Establishment of this pattern requires a shared signaling pathway in both groups of animals. Previous studies suggested that a shared signaling pathway functions in opposite ways in vertebrates and invertebrates, despite the final patterning outcomes having remained the same. Here, we employ bioinformatics, biochemistry, and transgenic animal technology to elucidate the genetic mechanism by which this pathway can engage the same components to generate opposite instructions and yet arrive at similar outcomes in patterning of the nervous system. Our findings highlight how natural selection can act to conserve a particular output pattern despite changes during evolution in the genetic mechanisms underlying the formation of this pattern.

Hemichordate neurulation and the origin of the neural tube

The origin of the body plan of our own phylum, Chordata, is one of the most fascinating questions in evolutionary biology. Yet, after more than a century of debate, the evolutionary origins of the neural tube and notochord remain unclear. Here we examine the development of the collar nerve cord in the hemichordate Balanoglossus simodensis and find shared gene expression patterns between hemichordate and chordate neurulation. Moreover, we show that the dorsal endoderm of the buccal tube and the stomochord expresses Hedgehog RNA, and it seems likely that collar cord cells can receive the signal. Our data suggest that the endoderm functions as an organizer to pattern the overlying collar cord, similar to the relationship between the notochord and neural tube in chordates. We propose that the origin of the core genetic mechanisms for the development of the notochord and the neural tube date back to the last common deuterostome ancestor.

Cleavage of the Drosophila screw prodomain is critical for a dynamic BMP morphogen gradient in embryogenesis

Dorsoventral patterning of the Drosophila embryo is regulated by graded distribution of bone morphogenetic proteins (BMPs) composed of two ligands, decapentaplegic (Dpp) a BMP2/4 ortholog and screw (Scw) a BMP5/6/7/8 family member. scw(E1) encodes an unusual allele that was isolated as a dominant enhancer of partial loss-of-function mutations in dpp. However, the molecular mechanisms that underlie this genetic interaction remain to be addressed. Here we show that scw(E1) contains a mutation at the furin cleavage site within the prodomain that is crucial for ligand production. Furthermore, our data show that Scw(E1) preferentially forms heterodimers with Dpp rather than homotypic dimers, providing a possible explanation for the dominant negative phenotype of scw(E1) alleles. The unprocessed prodomain of Scw(E1) remains in a complex with the Dpp:Scw heterodimer, and thus could interfere with interaction of the ligand with the extracellular matrix, or the kinetics of processing/secretion of the ligand in vivo. These data reveal novel mechanisms by which post-translational regulation of Scw can modulate Dpp signaling activity.

The evolutionary history of vertebrate cranial placodes II. Evolution of ectodermal patterning

Cranial placodes are evolutionary innovations of vertebrates. However, they most likely evolved by redeployment, rewiring and diversification of preexisting cell types and patterning mechanisms. In the second part of this review we compare vertebrates with other animal groups to elucidate the evolutionary history of ectodermal patterning. We show that several transcription factors have ancient bilaterian roles in dorsoventral and anteroposterior regionalisation of the ectoderm. Evidence from amphioxus suggests that ancestral chordates then concentrated neurosecretory cells in the anteriormost non-neural ectoderm. This anterior proto-placodal domain subsequently gave rise to the oral siphon primordia in tunicates (with neurosecretory cells being lost) and anterior (adenohypophyseal, olfactory, and lens) placodes of vertebrates. Likewise, tunicate atrial siphon primordia and posterior (otic, lateral line, and epibranchial) placodes of vertebrates probably evolved from a posterior proto-placodal region in the tunicate-vertebrate ancestor. Since both siphon primordia in tunicates give rise to sparse populations of sensory cells, both proto-placodal domains probably also gave rise to some sensory receptors in the tunicate-vertebrate ancestor. However, proper cranial placodes, which give rise to high density arrays of specialised sensory receptors and neurons, evolved from these domains only in the vertebrate lineage. We propose that this may have involved rewiring of the regulatory network upstream and downstream of Six1/2 and Six4/5 transcription factors and their Eya family cofactors. These proteins, which play ancient roles in neuronal differentiation were first recruited to the dorsal non-neural ectoderm in the tunicate-vertebrate ancestor but subsequently probably acquired new target genes in the vertebrate lineage, allowing them to adopt new functions in regulating proliferation and patterning of neuronal progenitors.

Size-dependent regulation of dorsal-ventral patterning in the early Drosophila embryo

How natural variation in embryo size affects patterning of the Drosophila embryo dorsal-ventral (DV) axis is not known. Here we examined quantitatively the relationship between nuclear distribution of the Dorsal transcription factor, boundary positions for several target genes, and DV axis length. Data were obtained from embryos of a wild-type background as well as from mutant lines inbred to size select embryos of smaller or larger sizes. Our data show that the width of the nuclear Dorsal gradient correlates with DV axis length. In turn, for some genes expressed along the DV axis, the boundary positions correlate closely with nuclear Dorsal levels and with DV axis length; while the expression pattern of others is relatively constant and independent of the width of the Dorsal gradient. In particular, the patterns of snail (sna) and ventral nervous system defective (vnd) correlate with nuclear Dorsal levels and exhibit scaling to DV length; while the pattern of intermediate neuroblasts defective (ind) remains relatively constant with respect to changes in Dorsal and DV length. However, in mutants that exhibit an abnormal expansion of the Dorsal gradient which fails to scale to DV length, only sna follows the Dorsal distribution and exhibits overexpansion; in contrast, vnd and ind do not overexpand suggesting some additional mechanism acts to refine the dorsal boundaries of these two genes. Thus, our results argue against the idea that the Dorsal gradient works as a global system of relative coordinates along the DV axis and suggest that individual targets respond to changes in embryo size in a gene-specific manner.

Kinetics of gene derepression by ERK signaling

ERK controls gene expression in development, but mechanisms that link ERK activation to changes in transcription are not well understood. We used high-resolution analysis of signaling dynamics to study transcriptional interpretation of ERK signaling during Drosophila embryogenesis, at a stage when ERK induces transcription of intermediate neuroblasts defective (ind), a gene essential for patterning of the nerve cord. ERK induces ind by antagonizing its repression by Capicua (Cic), a transcription factor that acts as a sensor of receptor tyrosine kinases in animal development and human diseases. A recent study established that active ERK reduces the nuclear levels of Cic, but it remained unclear whether this is required for the induction of Cic target genes. We provide evidence that Cic binding sites within the regulatory DNA of ind control the spatial extent and the timing of ind expression. At the same time, we demonstrate that ERK induces ind before Cic levels in the nucleus are reduced. Based on this, we propose that ERK-dependent relief of gene repression by Cic is a two-step process, in which fast reduction of repressor activity is followed by slower changes in nuclear localization and overall protein levels. This may be a common feature of systems in which ERK induces genes by relief of transcriptional repression.

Fine-tuned shuttles for bone morphogenetic proteins

Bone morphogenetic proteins (BMPs) are potent secreted signaling factors that trigger phosphorylation of Smad transcriptional regulators through receptor complex binding at the cell-surface. Resulting changes in target gene expression impact critical cellular responses during development and tissue homeostasis. BMP activity is tightly regulated in time and space by secreted modulators that control BMP extracellular distribution and availability for receptor binding. Such extracellular regulation is key for BMPs to function as morphogens and/or in the formation of morphogen activity gradients. Here, we review shuttling systems utilized to control the distribution of BMP ligands in tissue of various geometries, developing under different temporal constraints. We discuss the biological advantages for employing specific strategies for BMP shuttling and roles of varied ligand forms.

Variation in the dorsal gradient distribution is a source for modified scaling of germ layers in Drosophila

Specification of germ layers along the dorsoventral axis by morphogenetic gradients is an ideal model to study scaling properties of gradients and cell fate changes during evolution. Classical anatomical studies in divergent insects (e.g., flies and grasshoppers) revealed that the neuroectodermal size is conserved and originates similar numbers of neuroblasts of homologous identity. In contrast, mesodermal domains vary significantly in closely related Drosophila species. To further investigate the underlying mechanisms of scaling of germ layers across Drosophila species, we quantified the Dorsal (Dl)/NF-κB gradient, the main morphogenetic gradient that initiates separation of the mesoderm, neuroectoderm, and ectoderm. We discovered a variable range of Toll activation across species and found that Dl activates mesodermal genes at the same threshold levels in melanogaster sibling species. We also show that the Dl gradient distribution can be modulated by nuclear size and packing densities. We propose that variation in mesodermal size occurs at a fast evolutionary rate and is an important mechanism to define the ventral boundary of the neuroectoderm.

A Schnurri/Mad/Medea complex attenuates the dorsal-twist gradient readout at vnd

Morphogen gradients are used in developing embryos, where they subdivide a field of cells into territories characterized by distinct cell fate potentials. Such systems require both a spatially-graded distribution of the morphogen, and an ability to encode different responses at different target genes. However, the potential for different temporal responses is also present because morphogen gradients typically provide temporal cues, which may be a potential source of conflict. Thus, a low threshold response adapted for an early temporal onset may be inappropriate when the desired spatial response is a spatially-limited, high-threshold expression pattern. Here, we identify such a case with the Drosophila vnd locus, which is a target of the dorsal (dl) nuclear concentration gradient that patterns the dorsal/ventral (D/V) axis of the embryo. The vnd gene plays a critical role in the "ventral dominance" hierarchy of vnd, ind, and msh, which individually specify distinct D/V neural columnar fates in increasingly dorsal ectodermal compartments. The role of vnd in this regulatory hierarchy requires early temporal expression, which is characteristic of low-threshold responses, but its specification of ventral neurogenic ectoderm demands a relatively high-threshold response to dl. We show that the Neurogenic Ectoderm Enhancer (NEE) at vnd takes additional input from the complementary Dpp gradient via a conserved Schnurri/Mad/Medea silencer element (SSE) unlike NEEs at brk, sog, rho, and vn. These results show how requirements for conflicting temporal and spatial responses to the same gradient can be solved by additional inputs from complementary gradients.

Multi-modal effects of BMP signaling on Nodal expression in the lateral plate mesoderm during left-right axis formation in the chick embryo

During development of left-right asymmetry in the vertebrate embryo, Nodal plays a central role for determination of left-handedness. Bone morphogenetic protein (BMP) signaling has an important role for regulation of Nodal expression, although there is controversy over whether BMP signaling has a positive or negative effect on Nodal expression in the chick embryo. As BMP is a morphogen, we speculated that different concentrations might induce different responses in the cells of the lateral plate mesoderm (LPM). To test this hypothesis, we analyzed the effects of various concentrations of BMP4 and NOGGIN on Nodal expression in the LPM. We found that the effect on Nodal expression varied in a complex fashion with the concentration of BMP. In agreement with previous reports, we found that a high level of BMP signaling induced Nodal expression in the LPM, whereas a low level inhibited expression. However, a high intermediate level of BMP signaling was found to suppress Nodal expression in the left LPM, whereas a low intermediate level induced Nodal expression in the right LPM. Thus, the high and the low intermediate levels of BMP signaling up-regulated Nodal expression, but the high intermediate and low levels of BMP signaling down-regulated Nodal expression. Next, we sought to identify the mechanisms of this complex regulation of Nodal expression by BMP signaling. At the low intermediate level of BMP signaling, regulation depended on a NODAL positive-feedback loop suggesting the possibility of crosstalk between BMP and NODAL signaling. Overexpression of a constitutively active BMP receptor, a constitutively active ACTIVIN/NODAL receptor and SMAD4 indicated that SMAD1 and SMAD2 competed for binding to SMAD4 in the cells of the LPM. Nodal regulation by the high and low levels of BMP signaling was dependent on Cfc up-regulation or down-regulation, respectively. We propose a model for the variable effects of BMP signaling on Nodal expression in which different levels of BMP signaling regulate Nodal expression by a balance between BMP-pSMAD1/4 signaling and NODAL-pSMAD2/4 signaling.

BMP-dependent serosa and amnion specification in the scuttle fly Megaselia abdita

Bone morphogenetic protein (BMP) signaling is an essential factor in dorsoventral patterning of animal embryos but how BMP signaling evolved with fundamental changes in dorsoventral tissue differentiation is unclear. Flies experienced an evolutionary reduction of extra-embryonic tissue types from two (amniotic and serosal tissue) to one (amnionserosal tissue). BMP-dependent amnioserosa specification has been studied in Drosophila melanogaster. However, the mechanisms of serosal and amniotic tissue specification in less diverged flies remain unknown. To better understand potential evolutionary links between BMP signaling and extra-embryonic tissue specification, we examined the activity profile and function of BMP signaling in serosa and amnion patterning of the scuttle fly Megaselia abdita (Phoridae) and compared the BMP activity profiles between M. abdita and D. melanogaster. In blastoderm embryos of both species, BMP activity peaked at the dorsal midline. However, at the beginning of gastrulation, peak BMP activity in M. abdita shifted towards prospective amnion tissue. This transition correlated with the first signs of amnion differentiation laterally adjacent to the serosa anlage. Marker-assisted analysis of six BMP signaling components (dpp, gbb, scw, tkv, sax, sog) by RNA interference revealed that both serosa and amnion specification of M. abdita are dependent on BMP activity. Conversely, BMP gain-of-function experiments caused sharpened expression boundaries of extra-embryonic target genes indicative of positive feedback. We propose that changes in the BMP activity profile at the beginning of gastrulation might have contributed to the reduction of extra-embryonic tissue types during the radiation of cyclorrhaphan flies.

Ptychoderid hemichordate neurulation without a notochord

Enteropneust hemichordates share several characteristics with chordates, such as a Hox-specified anterior-posterior axis, pharyngeal gill slits, a dorsal central nervous system (CNS), and a juvenile postanal tail. Ptychoderid hemichordates, such as the indirect-developer Ptychodera flava, have feeding larvae and a remarkable capacity to regenerate their CNS. We compared neurulation of ptychoderid hemichordates and chordates using histological analyses, and found many similarities in CNS development. In ptychoderid hemichordates, which lack a notochord, the proboscis skeleton develops from endoderm after neurulation. The position of the proboscis skeleton directly under the nerve cord suggests that it serves a structural role similar to the notochord of chordates. These results suggest that either the CNS preceded evolution of the notochord or that the notochord has been lost in hemichordates. The evolution of the notochord remains ambiguous, but it may have evolved from endoderm, not mesoderm.

Evolutionary crossroads in developmental biology: annelids

Annelids (the segmented worms) have a long history in studies of animal developmental biology, particularly with regards to their cleavage patterns during early development and their neurobiology. With the relatively recent reorganisation of the phylogeny of the animal kingdom, and the distinction of the super-phyla Ecdysozoa and Lophotrochozoa, an extra stimulus for studying this phylum has arisen. As one of the major phyla within Lophotrochozoa, Annelida are playing an important role in deducing the developmental biology of the last common ancestor of the protostomes and deuterostomes, an animal from which >98% of all described animal species evolved.

Pattern formation by graded and uniform signals in the early Drosophila embryo

The early Drosophila embryo is patterned by graded distributions of maternal transcription factors. Recent studies revealed that pattern formation by these graded signals depends on uniformly expressed transcriptional activators, such as Zelda. Removal of Zelda influences both the timing and the spatial expression domains for most of the genes controlled by maternal gradients. We demonstrate that some of these patterning defects, which range from temporal delay to loss of expression, can be rationalized with the use of a mathematical model based on cooperative binding of graded and uniform factors. This model makes a number of predictions, which we confirm experimentally by analyzing the expression of short gastrulation (sog), a gene that is controlled by a combination of the Dorsal morphogen gradient and Zelda. The proposed model suggests a general mechanism for the formation of nested gene expression domains, which is a hallmark of tissue patterning by morphogen gradients. According to this mechanism, the differential effects of a morphogen on its target genes can depend on their differential sensitivity to uniform factors.

Lateral gene expression in Drosophila early embryos is supported by Grainyhead-mediated activation and tiers of dorsally-localized repression

The general consensus in the field is that limiting amounts of the transcription factor Dorsal establish dorsal boundaries of genes expressed along the dorsal-ventral (DV) axis of early Drosophila embryos, while repressors establish ventral boundaries. Yet recent studies have provided evidence that repressors act to specify the dorsal boundary of intermediate neuroblasts defective (ind), a gene expressed in a stripe along the DV axis in lateral regions of the embryo. Here we show that a short 12 base pair sequence ("the A-box") present twice within the ind CRM is both necessary and sufficient to support transcriptional repression in dorsal regions of embryos. To identify binding factors, we conducted affinity chromatography using the A-box element and found a number of DNA-binding proteins and chromatin-associated factors using mass spectroscopy. Only Grainyhead (Grh), a CP2 transcription factor with a unique DNA-binding domain, was found to bind the A-box sequence. Our results suggest that Grh acts as an activator to support expression of ind, which was surprising as we identified this factor using an element that mediates dorsally-localized repression. Grh and Dorsal both contribute to ind transcriptional activation. However, another recent study found that the repressor Capicua (Cic) also binds to the A-box sequence. While Cic was not identified through our A-box affinity chromatography, utilization of the same site, the A-box, by both factors Grh (activator) and Cic (repressor) may also support a "switch-like" response that helps to sharpen the ind dorsal boundary. Furthermore, our results also demonstrate that TGF-β signaling acts to refine ind CRM expression in an A-box independent manner in dorsal-most regions, suggesting that tiers of repression act in dorsal regions of the embryo.

A computational statistics approach for estimating the spatial range of morphogen gradients

A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.

The evolution of nervous system patterning: insights from sea urchin development

Recent studies of the sea urchin embryo have elucidated the mechanisms that localize and pattern its nervous system. These studies have revealed the presence of two overlapping regions of neurogenic potential at the beginning of embryogenesis, each of which becomes progressively restricted by separate, yet linked, signals, including Wnt and subsequently Nodal and BMP. These signals act to specify and localize the embryonic neural fields - the anterior neuroectoderm and the more posterior ciliary band neuroectoderm - during development. Here, we review these conserved nervous system patterning signals and consider how the relationships between them might have changed during deuterostome evolution.

EvoD/Vo: the origins of BMP signalling in the neuroectoderm

The genetic systems controlling body axis formation trace back as far as the ancestor of diploblasts (corals, hydra, and jellyfish) and triploblasts (bilaterians). Comparative molecular studies, often referred to as evo-devo, provide powerful tools for elucidating the origins of mechanisms for establishing the dorsal-ventral and anterior-posterior axes in bilaterians and reveal differences in the evolutionary pressures acting upon tissue patterning. In this Review, we focus on the origins of nervous system patterning and discuss recent comparative genetic studies; these indicate the existence of an ancient molecular mechanism underlying nervous system organization that was probably already present in the bilaterian ancestor.

Divergent mechanisms specify chordate motoneurons: evidence from ascidians

Ascidians are members of the vertebrate sister group Urochordata. Their larvae exhibit a chordate body plan, which forms by a highly accelerated embryonic strategy involving a fixed cell lineage and small cell numbers. We report a detailed analysis of the specification of three of the five pairs of motoneurons in the ascidian Ciona intestinalis and show that despite well-conserved gene expression patterns and embryological outcomes compared with vertebrates, key signalling molecules have adopted different roles. We employed a combination of cell ablation and gene manipulation to analyse the function of two signalling molecules with key roles in vertebrate motoneuron specification that are known to be expressed equivalently in ascidians: the inducer Sonic hedgehog, produced ventrally by the notochord and floorplate; and the inhibitory BMP2/4, produced on the lateral/dorsal side of the neural plate. Our surprising conclusion is that neither BMP2/4 signalling nor the ventral cell lineages expressing hedgehog play crucial roles in motoneuron formation in Ciona. Furthermore, BMP2/4 overexpression induced ectopic motoneurons, the opposite of its vertebrate role. We suggest that the specification of motoneurons has been modified during ascidian evolution, such that BMP2/4 has adopted a redundant inductive role rather than a repressive role and Nodal, expressed upstream of BMP2/4 in the dorsal neural tube precursors, acts as a motoneuron inducer during normal development. Thus, our results uncover significant differences in the mechanisms used for motoneuron specification within chordates and also highlight the dangers of interpreting equivalent expression patterns as indicative of conserved function in evo-devo studies.

The evolution of dorsal-ventral patterning mechanisms in insects

The gene regulatory network (GRN) underpinning dorsal-ventral (DV) patterning of the Drosophila embryo is among the most thoroughly understood GRNs, making it an ideal system for comparative studies seeking to understand the evolution of development. With the emergence of widely applicable techniques for testing gene function, species with sequenced genomes, and multiple tractable species with diverse developmental modes, a phylogenetically broad and molecularly deep understanding of the evolution of DV axis formation in insects is feasible. Here, we review recent progress made in this field, compare our emerging molecular understanding to classical embryological experiments, and suggest future directions of inquiry.