A clock and trail model for somite formation, specialization and polarization

Sequential changes in cellular properties accompanying amniote somite formation

Somites are transient structures derived from the pre-somitic mesoderm (PSM), involving mesenchyme-to-epithelial transition (MET) where the cells change their shape and polarize. Using Scanning electron microscopy (SEM), immunocytochemistry and confocal microscopy, we study the progression of these events along the tail-to-head axis of the embryo, which mirrors the progression of somitogenesis (younger cells located more caudally). SEM revealed that PSM epithelialization is a gradual process, which begins much earlier than previously thought, starting with the dorsalmost cells, then the medial ones, and then, simultaneously, the ventral and lateral cells, before a somite fully separates from the PSM. The core (internal) cells of the PSM and somites never epithelialize, which suggests that the core cells could be 'trapped' within the somitocoele after cells at the surfaces of the PSM undergo MET. Three-dimensional imaging of the distribution of the cell polarity markers PKCζ, PAR3, ZO1, the Golgi marker GM130 and the apical marker N-cadherin reveal that the pattern of polarization is distinctive for each marker and for each surface of the PSM, but the order of these events is not the same as the progression of cell elongation. These observations challenge some assumptions underlying existing models of somite formation.

Cellular aspects of somite formation in vertebrates

Vertebrate segmentation, the process that generates a regular arrangement of somites and thereby establishes the pattern of the adult body and of the musculoskeletal and peripheral nervous systems, was noticed many centuries ago. In the last few decades, there has been renewed interest in the process and especially in the molecular mechanisms that might account for its regularity and other spatial-temporal properties. Several models have been proposed but surprisingly, most of these do not provide clear links between the molecular mechanisms and the cell behaviours that generate the segmental pattern. Here we present a short survey of our current knowledge about the cellular aspects of vertebrate segmentation and the similarities and differences between different vertebrate groups in how they achieve their metameric pattern. Taking these variations into account should help to assess each of the models more appropriately.

Role of β-Catenin Activation Levels and Fluctuations in Controlling Cell Fate

Cells have developed numerous adaptation mechanisms to external cues by controlling signaling-pathway activity, both qualitatively and quantitatively. The Wnt/β-catenin pathway is a highly conserved signaling pathway involved in many biological processes, including cell proliferation, differentiation, somatic cell reprogramming, development, and cancer. The activity of the Wnt/β-catenin pathway and the temporal dynamics of its effector β-catenin are tightly controlled by complex regulations. The latter encompass feedback loops within the pathway (e.g., a negative feedback loop involving Axin2, a β-catenin transcriptional target) and crosstalk interactions with other signaling pathways. Here, we provide a review shedding light on the coupling between Wnt/β-catenin activation levels and fluctuations across processes and cellular systems; in particular, we focus on development, in vitro pluripotency maintenance, and cancer. Possible mechanisms originating Wnt/β-catenin dynamic behaviors and consequently driving different cellular responses are also reviewed, and new avenues for future research are suggested.

Multiple roles of timing in somite formation

During development, vertebrate embryos produce serially repeated elements, the somites, on each side of the midline. These generate the vertebral column, skeletal musculature and dermis. They form sequentially, one pair at a time, from mesenchymal tissue near the tail. Somite development is a complex process. The embryo must control the number, size, and timing of somite formation, their subdivision into functional regions along three axes, regional identity such that somites develop in a region-specific way, and interactions with neighbouring tissues that coordinate them with nearby structures. Here we discuss many timing-related mechanisms that contribute to set up the spatial pattern.

ONE-DIMENSIONAL MODEL OF SOMITIC CELLS POLARIZATION IN A BISTABILITY WINDOW OF EMBRYONIC MESODERM

The considerations are based on the understanding that somitic cells polarization in bistability window of embryonic (pre-somitic) mesoderm is a dynamical process. It occurs in the form of a polarization wavefront of somite cells spread in anterior–posterior direction of the embryonic mesoderm. It is assumed that a macroscopic cell polarization has a bistable behavior corresponding to the molecular mechanism of bistability window formation. Moreover this type of polarization is supposed to be transmittable to the other cells by contact interaction. At the end, a volume of polarized cells is taken, which is able to create mechanical tension in the volume of nonpolarized neighbor cells and to inhibit their polarization. On this basis we explore the leading aspect of somitogenesis robustness by considering a simple wavefront model of polarization and analyzing its propagation in terms of the standard methods of qualitative theory of differential equations. The obtained theoretical results are interpreted in the context of their possible experimental verification.

Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability

A major goal of evolutionary developmental biology (evo-devo) is to understand how multicellular body plans of increasing complexity have evolved, and how the corresponding developmental programs are genetically encoded. It has been repeatedly argued that key to the evolution of increased body plan complexity is the modularity of the underlying developmental gene regulatory networks (GRNs). This modularity is considered essential for network robustness and evolvability. In our opinion, these ideas, appealing as they may sound, have not been sufficiently tested. Here we use computer simulations to study the evolution of GRNs' underlying body plan patterning. We select for body plan segmentation and differentiation, as these are considered to be major innovations in metazoan evolution. To allow modular networks to evolve, we independently select for segmentation and differentiation. We study both the occurrence and relation of robustness, evolvability and modularity of evolved networks. Interestingly, we observed two distinct evolutionary strategies to evolve a segmented, differentiated body plan. In the first strategy, first segments and then differentiation domains evolve (SF strategy). In the second scenario segments and domains evolve simultaneously (SS strategy). We demonstrate that under indirect selection for robustness the SF strategy becomes dominant. In addition, as a byproduct of this larger robustness, the SF strategy is also more evolvable. Finally, using a combined functional and architectural approach, we determine network modularity. We find that while SS networks generate segments and domains in an integrated manner, SF networks use largely independent modules to produce segments and domains. Surprisingly, we find that widely used, purely architectural methods for determining network modularity completely fail to establish this higher modularity of SF networks. Finally, we observe that, as a free side effect of evolving segmentation and differentiation in combination, we obtained in-silico developmental mechanisms resembling mechanisms used in vertebrate development.

Random cell movement promotes synchronization of the segmentation clock

In vertebrate somitogenesis, the expression of segmentation clock genes oscillates and the oscillation is synchronized over nearby cells. Both experimental and theoretical studies have shown that the synchronization among cells is realized by intercellular interaction via Delta-Notch signaling. However, the following questions emerge: (i) During somitogenesis, dynamic rearrangement of relative cell positions is observed in the posterior presomitic mesoderm. Can a synchronized state be stably sustained under random cell movement? (ii) Experimental studies have reported that the synchronization of cells can be recovered in about 10 or fewer oscillation cycles after the complete loss of synchrony. However, such a quick recovery of synchronization is not possible according to previous theoretical models. In this paper, we first show by numerical modeling that synchronized oscillation can be sustained under random cell movement. We also find that for initial perturbation, the synchronization of cells is recovered much faster and it is for a wider range of reaction parameters than the case without cell movement. When the posterior presomitic mesoderm is rectangular, faster synchronization is achieved if cells exchange their locations more with neighbors located along the longer side of the domain. Finally, we discuss that the enhancement of synchronization by random cell movement occurs in several different models for the oscillation of segmentation clock genes.

Spatiotemporal pattern in somitogenesis: a non-Turing scenario with wave propagation

Living organisms maintain their lives under far-from-equilibrium conditions by creating a rich variety of spatiotemporal structures in a self-organized manner, such as temporal rhythms, switching phenomena, and development of the body. In this paper, we focus on the dynamical process of morphogens in somitogenesis in mice where propagation of the gene expression level plays an essential role in creating the spatially periodic patterns of the vertebral columns. We present a simple discrete reaction-diffusion model which includes neighboring interaction through an activator, but not diffusion of an inhibitor. We can produce stationary periodic patterns by introducing the effect of spatial discreteness to the field. Based on the present model, we discuss the underlying physical principles that are independent of the details of biomolecular reactions. We also discuss the framework of spatial discreteness based on the reaction-diffusion model in relation to a cellular array, by comparison with an actual experimental observation.

Human embryonic stem cell-derived mesenchymal progenitors--potential in regenerative medicine

Tissue engineering and cell therapy require large-scale production of homogeneous populations of lineage-restricted progenitor cells that easily can be induced to differentiate into a specific tissue. We have developed straightforward protocols for the establishment of human embryonic stem (hES) cell-derived mesenchymal progenitor (hES-MP) cell lines. The reproducibility was proven by derivation of multiple hES-MP cell lines from 10 different hES cell lines. To illustrate clinical applicability, a xeno-free hES-MP cell line was also derived. None of the markers characteristic for undifferentiated hES cells were detected in the hES-MP cells. Instead, these cells were highly similar to mesenchymal stem cells with regard to morphology and expression of markers. The safety of hES-MP cells following transplantation was studied in severely combined immunodeficient (SCID) mice. The implanted hES-MP cells gave rise to homogeneous, well-differentiated tissues exclusively of mesenchymal origin and no teratoma formation was observed. These cells further have the potential to differentiate toward the osteogenic, adipogenic, and chondrogenic lineages in vitro. The possibility of easily and reproducibly generating highly expandable hES-MP cell lines from well-characterized hES cell lines with differentiation potential into several mesodermal tissues entails an enormous potential for the field of regenerative medicine.

Traveling wave formation in vertebrate segmentation

In vertebrate somitogenesis, "segmentation clock" genes (such as her in zebrafish, hairy in chick, and hes in mouse) show oscillation, synchronized over nearby cells through cell-cell interaction. The locations of high gene expression appear with regular intervals and move like a wave from posterior to anterior with the speed slowing down toward the anterior end. We analyze traveling wave pattern of her gene expression when there is an anterior-posterior gradient of one of the reaction rates in the gene-protein kinetics. We adopt a model which includes the kinetics of mRNA and proteins of her gene in each cell and cell-cell interaction by Delta-Notch system explicitly. We show that the observed spatio-temporal pattern can be explained if mRNA degradation, protein translation, protein transportation to nucleus occurs faster, or mRNA transcription, Delta protein synthesis occurs slower in posterior than in anterior regions. All of these gradients are those that produce longer periodicity of oscillation of clock gene expression in the anterior than in the posterior. Based on this result, we derive a mathematical formula for how the peak of gene expression moves along the pre-somitic mesoderm.

Somite cell cycle analysis using somite-staging to measure intrinsic developmental time

Somite stages were employed as units of intrinsic developmental time to measure cell doubling rate and other cell cycle parameters of chick forelimb level somites. Somite cell nuclei doubled over an interval corresponding to approximately 7+ somite stages (7+ ss; approximately 11 hr) and approximately 24 new primary myotome cells are born per somite stage ( approximately 16/hr). FACS analysis of DNA content in dissociated paraxial mesoderm cells indicated that slightly more than half are in G1/G0 phase of the cell cycle and that the average combined length of the S phase and G2 phase intervals is approximately 3 ss ( approximately 4.5 hr). A wavefront of increased mitotic nuclei per segment coincident with somite budding potentially reflects a surge in the number of cells entering S phase 3 ss earlier as each PSM segment becomes unresponsive to FGF signaling as it passes through the determination front.

Oscillatory lunatic fringe activity is crucial for segmentation of the anterior but not posterior skeleton

The Notch pathway plays multiple roles during vertebrate somitogenesis,functioning in the segmentation clock and during rostral/caudal (R/C) somite patterning. Lunatic fringe (Lfng) encodes a glycosyltransferase that modulates Notch signaling, and its expression patterns suggest roles in both of these processes. To dissect the roles played by Lfng during somitogenesis, a novel allele was established that lacks cyclic Lfngexpression within the segmentation clock, but that maintains expression during R/C somite patterning (LfngΔFCE1). In the absence of oscillatory Lfng expression, Notch activation is ubiquitous in the PSM of LfngΔFCE1 embryos. LfngΔFCE1 mice exhibit severe segmentation phenotypes in the thoracic and lumbar skeleton. However, the sacral and tail vertebrae are only minimally affected in LfngΔFCE1mice, suggesting that oscillatory Lfng expression and cyclic Notch activation are important in the segmentation of the thoracic and lumbar axial skeleton (primary body formation), but are largely dispensable for the development of sacral and tail vertebrae (secondary body formation). Furthermore, we find that the loss of cyclic Lfng has distinct effects on the expression of other clock genes during these two stages of development. Finally, we find that LfngΔFCE1 embryos undergo relatively normal R/C somite patterning, confirming that Lfngroles in the segmentation clock are distinct from its functions in somite patterning. These results suggest that the segmentation clock may employ varied regulatory mechanisms during distinct stages of anterior/posterior axis development, and uncover previously unappreciated connections between the segmentation clock, and the processes of primary and secondary body formation.

Avian somitogenesis: translating time and space into pattern

Vertebrates have a metameric bodyplan that is based on the presence of paired somites. Somites develop from the segmental plate in a cranio-caudal sequence. At the same time, new material is added from Hensen's node, the primitive streak and the tailbud. In this way, the material residing in the segmental plate remains constant and comprises 12 prospective somites on each side. Prospective segment borders are not yet determined in the caudal segmental plate. Prior to segmentation, the cranial segmental plate undergoes epithelialization, which is controlled by signals from the neural tube and ectoderm. The bHLH transcription factor Paraxis is critically involved in this process. Formation of a new somite from the cranial end of the segmental plate is a highly controlled process involving complex cell movements in relation to each other. Hox genes specify regional identity of the somites and their derivatives. In the chicken a transposition of thoracic into cervical vertebrae has occurred as compared to the mouse. Transcription factors of the bHLH and homeodomain type also specify the cranio-caudal polarity and that of particular cell groups within the somites. According to segmentation models, somitogenesis is under the control of a "segmentation clock" in combination with a morphogen gradient. This hypothesis has recently found support from molecular data, especially the cycling expression of genes such as cHairy1 and Lunatic Fringe, which depend on the Notch/Delta pathway of signal transduction. FGF8 has been described to be distributed along a cranio-caudal gradient. The first oscillating gene described shown to be independent of Notch is Axin2, encoding a negative regulator of the canonical Wnt pathway and a target of Wnt3a. Wnt3a and Axin2 show a similar distribution as FGF8 with high levels in the tailbud. The chick embryo has recently become accessible to molecular approaches such as overexpression by electroporation and RNA interference which can be expected to help elucidating some of the still open questions concerning somitogenesis.

Deriving structure from evolution: metazoan segmentation

Segmentation is a common feature of disparate clades of metazoans, and its evolution is a central problem of evolutionary developmental biology. We evolved in silico regulatory networks by a mutation/selection process that just rewards the number of segment boundaries. For segmentation controlled by a static gradient, as in long-germ band insects, a cascade of adjacent repressors reminiscent of gap genes evolves. For sequential segmentation controlled by a moving gradient, similar to vertebrate somitogenesis, we invariably observe a very constrained evolutionary path or funnel. The evolved state is a cell autonomous 'clock and wavefront' model, with the new attribute of a separate bistable system driven by an autonomous clock. Early stages in the evolution of both modes of segmentation are functionally similar, and simulations suggest a possible path for their interconversion. Our computation illustrates how complex traits can evolve by the incremental addition of new functions on top of pre-existing traits.

Molecular basis for skeletal variation: insights from developmental genetic studies in mice

Skeletal variations are common in humans, and potentially are caused by genetic as well as environmental factors. We here review molecular principles in skeletal development to develop a knowledge base of possible alterations that could explain variations in skeletal element number, shape or size. Environmental agents that induce variations, such as teratogens, likely interact with the molecular pathways that regulate skeletal development.

From segment to somite: segmentation to epithelialization analyzed within quantitative frameworks

One of the most visually striking patterns in the early developing embryo is somite segmentation. Somites form as repeated, periodic structures in pairs along nearly the entire caudal vertebrate axis. The morphological process involves short- and long-range signals that drive cell rearrangements and cell shaping to create discrete, epithelialized segments. Key to developing novel strategies to prevent somite birth defects that involve axial bone and skeletal muscle development is understanding how the molecular choreography is coordinated across multiple spatial scales and in a repeating temporal manner. Mathematical models have emerged as useful tools to integrate spatiotemporal data and simulate model mechanisms to provide unique insights into somite pattern formation. In this short review, we present two quantitative frameworks that address the morphogenesis from segment to somite and discuss recent data of segmentation and epithelialization.

The vertebrate segmentation clock and its role in skeletal birth defects

The segmental structure of the vertebrate body plan is most evident in the axial skeleton. The regulated generation of somites, a process called somitogenesis, underlies the vertebrate body plan and is crucial for proper skeletal development. A genetic clock regulates this process, controlling the timing of somite development. Molecular evidence for the existence of the segmentation clock was first described in the expression of Notch signaling pathway members, several of which are expressed in a cyclic fashion in the presomitic mesoderm (PSM). The Wnt and fibroblast growth factor (FGF) pathways have also recently been linked to the segmentation clock, suggesting that a complex, interconnected network of three signaling pathways regulates the timing of somitogenesis. Mutations in genes that have been linked to the clock frequently cause abnormal segmentation in model organisms. Additionally, at least two human disorders, spondylocostal dysostosis (SCDO) and Alagille syndrome (AGS), are caused by mutations in Notch pathway genes and exhibit vertebral column defects, suggesting that mutations that disrupt segmentation clock function in humans can cause congenital skeletal defects. Thus, it is clear that the correct, cyclic function of the Notch pathway within the vertebrate segmentation clock is essential for proper somitogenesis. In the future, with a large number of additional cyclic genes recently identified, the complex interactions between the various signaling pathways making up the segmentation clock will be elucidated and refined.

Repressor dimerization in the zebrafish somitogenesis clock

The oscillations of the somitogenesis clock are linked to the fundamental process of vertebrate embryo segmentation, yet little is known about their generation. In zebrafish, it has been proposed that Her proteins repress the transcription of their own mRNA. However, in its simplest form, this model is incompatible with the fact that morpholino knockdown of Her proteins can impair expression of their mRNA. Simple self-repression models also do not account for the spatiotemporal pattern of gene expression, with waves of gene expression shrinking as they propagate. Here we study computationally the networks generated by the wealth of dimerization possibilities amongst transcriptional repressors in the zebrafish somitogenesis clock. These networks can reproduce knockdown phenotypes, and strongly suggest the existence of a Her1–Her7 heterodimer, so far untested experimentally. The networks are the first reported to reproduce the spatiotemporal pattern of the zebrafish somitogenesis clock; they shed new light on the role of Her13.2, the only known link between the somitogenesis clock and positional information in the paraxial mesoderm. The networks can also account for perturbations of the clock by manipulation of FGF signaling. Achieving an understanding of the interplay between clock oscillations and positional information is a crucial first step in the investigation of the segmentation mechanism.

Vertebrate embryos acquire a segmented structure along the anteroposterior axis. Segmentation is critical for patterning of other structures (such as nerves, vertebrae, muscles, and blood vessels) and occurs by the rhythmic separation of balls of cells, called somites, from the anterior end of their precursor tissue, called the presomitic mesoderm. These rhythmic events are associated with oscillatory gene expression in the presomitic mesoderm: waves of gene expression originate at the posterior end and spread anteriorly. When a wave reaches the anterior end, a pair of new somites detaches. The set of genes whose expression oscillates is termed the “somitogenesis clock.” Even though the zebrafish somitogenesis clock has been the subject of intensive study, it is not clear how its oscillations are generated. It has been proposed that the mechanism involves a simple negative feedback loop, with proteins of the Her family periodically repressing their own expression. However, this is incompatible with some experimental results and does not explain how the spatiotemporal pattern of gene expression is generated. Here I propose a model—based on physical interactions between Her proteins—that is compatible with experimental results, and that explains how positional information is used to generate the spatiotemporal pattern of gene expression.

Understanding the somitogenesis clock: what's missing?

The segmentation of vertebrate embryos depends on a complex genetic network that generates highly dynamic gene expression. Many of the elements of the network have been identified, but their interaction and their influence on segmentation remain poorly understood. A few mathematical models have been proposed to explain the dynamics of subsets of the network, but the mechanistic bases remain controversial. This review focuses on outstanding problems with the generation of somitogenesis clock oscillations, and the ways they could regulate segmentation. Proposals that oscillations are generated by a negative feedback loop formed by Lunatic fringe and Notch signaling are weighed against a model based on positive feedback, and the experimental basis for models of simple negative feedback involving Her/Hes genes or Wnt targets is evaluated. Differences are then made explicit between the many 'clock and wavefront' model variants that have been proposed to explain how the clock regulates segmentation. An understanding of the somitogenesis clock will require addressing experimentally the many questions that arise from the study of simple models.

The genetics and embryology of zebrafish metamerism

Somites are the most obvious metameric structures in the vertebrate embryo. They are mesodermal segments that form in bilateral pairs flanking the notochord and are created sequentially in an anterior to posterior sequence concomitant with the posterior growth of the trunk and tail. Zebrafish somitogenesis is regulated by a clock that causes cells in the presomitic mesoderm (PSM) to undergo cyclical activation and repression of several notch pathway genes. Coordinated oscillation among neighboring cells manifests as stripes of gene expression that pass through the cells of the PSM in a posterior to anterior direction. As axial growth continually adds new cells to the posterior tail bud, cells of the PSM become relatively less posterior. This gradual assumption of a more anterior position occurs over developmental time and constitutes part of a maturation process that governs morphological segmentation in conjunction with the clock. Segment morphogenesis involves a mesenchymal to epithelial transition as prospective border cells at the anterior end of the mesenchymal PSM adopt a polarized, columnar morphology and surround a mesenchymal core of cells. The segmental pattern influences the development of the somite derivatives such as the myotome, and the myotome reciprocates to affect the formation of segment boundaries. While somites appear to be serially homologous, there may be variation in the segmentation mechanism along the body axis. Moreover, whereas the genetic architecture of the zebrafish, mouse, and chick segmentation clocks shares many common elements, there is evidence that the gene networks have undergone independent modification during evolution.

A Molecular Clock Operates During Chick Autopod Proximal-distal Outgrowth

Temporal control can be considered the fourth dimension in embryonic development. The identification of the somitogenesis molecular clock provided new insight into how embryonic cells measure time. We provide the first evidence of a molecular clock operating during chick fore-limb autopod outgrowth and patterning, by showing that the expression of the somitogenesis clock component hairy2 cycles in autopod chondrogenic precursor cells with a 6 h periodicity. We determined the length of time required to form an autopod skeletal limb element, and established a correlation between the latter and the periodicity of cyclic hairy2 gene expression. We suggest that temporal control exerted by cyclic gene expression can be a widespread mechanism providing cellular temporal information during vertebrate embryonic development.

Practical Lessons from Theoretical Models about the Somitogenesis

Vertebrae and other mammalian repetitive structures are formed from embryonic organs called somites. Somites arise sequentially from the unsegmented presomitic mesoderm (PSM). In mice, a new bilateral pair of somites arise every two hours from the rostral PSM. On the other hand, cells are added to the caudal side of the PSM due to cell proliferation of the tail bud. Somite formation correlates with cycles of cell-autonomous expression in the PSM of genes like Hes7. Because the somitogenesis is a highly dynamic and coordinated process, this event has been subjected to extensive theoretical modeling. Here, we describe the current understanding about the somitogenesis in mouse embryos with an emphasis on insights gained from computer simulations. It is worth noting that the combination of experiments and computer simulations has uncovered dynamical properties of the somitogenesis clock such as the transcription/translation delays, the half-life and the synchronization mechanism across the PSM. Theoretical models have also been useful to provide predictions and rigorous hypothesis about poorly understood processes such as the mechanisms by which the temporal PSM oscillations are arrested and converted into an spatial pattern. We aim at reviewing this theoretical literature in such a way that experimentalists might appreciate the resulting conclusions.

Segmentation in vertebrates: clock and gradient finally joined

The vertebral column is derived from somites formed by segmentation of presomitic mesoderm, a fundamental process of vertebrate embryogenesis. Models on the mechanism controlling this process date back some three to four decades. Access to understanding the molecular control of somitogenesis has been gained only recently by the discovery of molecular oscillators (segmentation clock) and gradients of signaling molecules, as predicted by early models. The Notch signaling pathway is linked to the oscillator and plays a decisive role in inter- and intrasomitic boundary formation. An Fgf8 signaling gradient is involved in somite size control. And the (canonical) Wnt signaling pathway, driven by Wnt3a, appears to integrate clock and gradient in a global mechanism controlling the segmentation process. In this review, we discuss recent advances in understanding the molecular mechanism controlling somitogenesis.

The chick embryo: a leading model in somitogenesis studies

The vertebrate body is built on a metameric organization which consists of a repetition of functionally equivalent units, each comprising a vertebra, its associated muscles, peripheral nerves and blood vessels. This periodic pattern is established during embryogenesis by the somitogenesis process. Somites are generated in a rhythmic fashion from the presomitic mesoderm and they subsequently differentiate to give rise to the vertebrae and skeletal muscles of the body. Somitogenesis has been very actively studied in the chick embryo since the 19th century and many of the landmark experiments that led to our current understanding of the vertebrate segmentation process have been performed in this organism. Somite formation involves an oscillator, the segmentation clock whose periodic signal is converted into the periodic array of somite boundaries by a spacing mechanism relying on a traveling threshold of FGF signaling regressing in concert with body axis extension.

Control of chemical pattern formation by a clock-and-wavefront type mechanism

The segmentation of many animals ranging from insects to mammals involves the sequential formation of stationary stripes of gene expression that are perpendicular to the growth axis of the developing embryo. This process has been accounted for by a variety of theoretical "clock-and-wavefront" type models that involve the arrest of an oscillation (the clock) at a moving boundary (the wavefront). Here, we demonstrate experimentally that progressive arrest of a homogeneous oscillation can control the symmetry as well as the wavelength of spatial structures in a chemical system. We show how a spontaneously formed, labyrinthine pattern can be converted into a pattern composed of ordered, parallel stripes and confirm a previously predicted proportionality between the wavelength and the period of the homogeneous oscillation. Our experiments provide the first experimental demonstration of a general mechanism for the control of pattern formation that has been hypothesized to operate in the context of biological morphogenesis.

A Notch feeling of somite segmentation and beyond

Vertebrate segmentation is manifested during embryonic development as serially repeated units termed somites that give rise to vertebrae, ribs, skeletal muscle and dermis. Many theoretical models including the "clock and wavefront" model have been proposed. There is compelling genetic evidence showing that Notch-Delta signaling is indispensable for somitogenesis. Notch receptor and its target genes, Hairy/E(spl) homologues, are known to be crucial for the ticking of the segmentation clock. Through the work done in mouse, chick, Xenopus and zebrafish, an oscillator operated by cyclical transcriptional activation and delayed negative feedback regulation is emerging as the fundamental mechanism underlying the segmentation clock. Ubiquitin-dependent protein degradation and probably other posttranslational regulations are also required. Fgf8 and Wnt3a gradients are important in positioning somite boundaries and, probably, in coordinating tail growth and segmentation. The circadian clock is another biochemical oscillator, which, similar to the segmentation clock, is operated with a negative transcription-regulated feedback mechanism. While the circadian clock uses a more complicated network of pathways to achieve homeostasis, it appears that the segmentation clock exploits the Notch pathway to achieve both signal generation and synchronization. We also discuss mathematical modeling and future directions in the end.

Segmentation and zooid formation in animals with a posterior growing region: the case for metabolic gradients and Turing waves

The discovery of periodic propagation of anteriorly moving pulses/stripes of gene expression in the presomitic mesoderm (PSM) of vertebrates has given new life to the clock and wavefront model, and other models of morphogenesis based on a molecular oscillator where the time periodicity is translated into spatial periodicity. Instead we suggest that segmentation, somitogenesis and metamerism in vertebrates and in invertebrates with a posterior growing region are based on a Turing-Child metabolic gradient that is progressively shifted posteriorly with the PSM as elongation, segmentation and somitogenesis proceed. This gradient corresponds to anteriorly propagating metabolic front in the PSM that drives the anteriorly propagating mRNA synthesis and which, together with mRNA degradation, explains stripe formation and spatial periodicity.The process of segmentation has been compared to zooid formation. We show that for annelids the metabolic profile behaves as a Turing field in the sense that an increase in the length of the system or a decrease of the Turing wavelength results in an additional peak in the posterior growing region as predicted by Turing theory. In particular, it is shown that the metabolic gradient that drives the segmentation is based on a Turing system.

Modulation of Notch Signaling During Somitogenesis

The Notch signaling pathway is known to govern various aspects of tissue differentiation during embryonic development by mediating local cell-cell interactions that often control cell fate. The conserved components that underlie Notch signaling have been isolated in vertebrates, leading to a biochemical delineation of a core Notch signaling pathway and functional studies of this pathway during embryogenesis. Herein we highlight recent progress in determining how Notch signaling contributes to the development of the vertebrate embryo. We first discuss the role of Notch in the process of segmentation where rapid changes have been shown to occur in both the spatial and temporal aspects of Notch signaling, which are critical for segmental patterning. Indeed, the role of Notch in segmentation re-emphasizes a recurring question in Notch biology: how are the components involved in Notch signaling regulated to ensure their dynamic properties? Second, we address this question by discussing recent work on the biochemical mechanisms that potentially regulate Notch signaling during segmentation, including those that act on the receptors, ligands, and signal transduction apparatus.

Somitogenesis: breaking new boundaries

Segmentation is a fundamental process in vertebrate embryogenesis, and one of the earliest manifestations of segmental patterning is the generation of transient, serially repeated blocks of mesodermal cells known as somites. Disruption of the normal segmentation process in humans leads to vertebral abnormalities such as spondylocostal dysostosis. In this minireview, we discuss recent advances in the dynamic molecular and cellular mechanisms governing segmentation.

Is the somitogenesis clock really cell-autonomous? A coupled-oscillator model of segmentation

A striking pattern of oscillatory gene expression, related to the segmentation process (somitogenesis), has been identified in chick, mouse, and zebrafish embryos. Somitogenesis displays great autonomy, and it is generally assumed in the literature that somitogenesis-related oscillations are cell-autonomous in chick and mouse. We point out in this article that there would be many biological reasons to expect some mechanism of coupling between cellular oscillators, and we present a model with such coupling, but which also has autonomous properties. Previous experiments can be re-interpreted in light of this model, showing that it is possible to reconcile both autonomous and non-autonomous aspects. We also show that experimental data, previously interpreted as supporting a purely negative-feedback model for the mechanism of the oscillations, is in fact more compatible with this new model, which relies essentially on positive feedback.

Wnt3a plays a major role in the segmentation clock controlling somitogenesis

The vertebral column derives from somites generated by segmentation of presomitic mesoderm (PSM). Somitogenesis involves a molecular oscillator, the segmentation clock, controlling periodic Notch signaling in the PSM. Here, we establish a novel link between Wnt/beta-catenin signaling and the segmentation clock. Axin2, a negative regulator of the Wnt pathway, is directly controlled by Wnt/beta-catenin and shows oscillating expression in the PSM, even when Notch signaling is impaired, alternating with Lfng expression. Moreover, Wnt3a is required for oscillating Notch signaling activity in the PSM. We propose that the segmentation clock is established by Wnt/beta-catenin signaling via a negative-feedback mechanism and that Wnt3a controls the segmentation process in vertebrates.

Cell dynamics during somite boundary formation revealed by time-lapse analysis

We follow somite segmentation in living chick embryos and find that the shaping process is not a simple periodic slicing of tissue blocks but a much more carefully choreographed separation in which the somite pulls apart from the segmental plate. Cells move across the presumptive somite boundary and violate gene expression boundaries thought to correlate with the site of the somite boundary. Similarly, cells do not appear to be preassigned to a given somite as they leave the node. The results offer a detailed picture of somite shaping and provide a spatiotemporal framework for linking gene expression with cell movements.

Limb patterning: reports of model's death exaggerated

The progress zone model for the specification of positional values for patterning the proximodistal axis of the vertebrate limb has been questioned, but the results can be largely reconciled with the old model.

Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis

Somitogenesis requires a segmentation clock and Notch signaling. Lunatic fringe (Lfng) expression in the presomitic mesoderm (PSM) cycles in the posterior PSM, is refined in the segmenting somite to the rostral compartment, and is required for segmentation. We identify distinct cis-acting regulatory elements for each aspect of Lfng expression. Fringe clock element 1 (FCE1) represents a conserved 110 bp region that is necessary to direct cyclic Lfng RNA expression in the posterior PSM. Mutational analysis of E boxes within FCE1 indicates a potential interplay of positive and negative transcriptional regulation by cyclically expressed bHLH proteins. A separable Lfng regulatory region directs expression to the prospective rostral aspect of the condensing somite. These independent Lfng regulatory cassettes advance a molecular framework for deciphering somite segmentation.

Vertebrate somitogenesis

In vertebrates, the paraxial mesoderm corresponds to the bilateral strips of mesodermal tissue flanking the notochord and neural tube and which are delimited laterally by the intermediate mesoderm and the lateral plate. The paraxial mesoderm comprises the head or cephalic mesoderm anteriorly and the somitic region throughout the trunk and the tail of the vertebrates. Soon after gastrulation, the somitic region of vertebrates starts to become segmented into paired blocks of mesoderm, termed somites. This process lasts until the number of somites characteristic of the species is reached. The somites later give rise to all skeletal muscles of the body, the axial skeleton, and part of the dermis. In this review I discuss the processes involved in the formation of the paraxial mesoderm and its segmentation into somites in vertebrates.

A cellular oscillator model for periodic pattern formation

In this paper, we present a model for pattern formation in developing organisms that is based on cellular oscillators (CO). An oscillatory process within cells serves as a developmental clock whose period is tightly regulated by cell autonomous or non-autonomous mechanisms. A spatial pattern is generated as a result of an initial temporal ordering of the cell oscillators freezing into spatial order as the clocks slow down and stop at different times or phases in their cycles. We apply a CO model to vertebrate somitogenesis and show that we can reproduce the dynamics of periodic gene expression patterns observed in the pre-somitic mesoderm. We also show how varying somite lengths can be generated with the CO model. We then discuss the model in view of experimental evidence and its relevance to other instances of biological pattern formation, showing its versatility as a pattern generator.

The making of the somite: molecular events in vertebrate segmentation

The reiterated structures of the vertebrate axial skeleton, spinal nervous system and body muscle are based on the metameric structure of somites, which are formed in a dynamic morphogenetic process. Somite segmentation requires the activity of a biochemical oscillator known as the somite-segmentation clock. Although the molecular identity of the clock remains unknown, genetic and experimental evidence has accumulated that indicates how the periodicity of somite formation is generated, how the positions of segment borders are determined, and how the rostrocaudal polarity within somite primordia is generated.

The winged helix transcription factor Foxc1a is essential for somitogenesis in zebrafish

Previous studies identified zebrafish foxc1a and foxc1b as homologs of the mouse forkhead gene, Foxc1. Both genes are transcribed in the unsegmented presomitic mesoderm (PSM), newly formed somites, adaxial cells, and head mesoderm. Here, we show that inhibiting synthesis of Foxc1a (but not Foxc1b) protein with two different morpholino antisense oligonucleotides blocks formation of morphological somites, segment boundaries, and segmented expression of genes normally transcribed in anterior and posterior somites and expression of paraxis implicated in somite epithelialization. Patterning of the anterior PSM is also affected, as judged by the absence of mesp-b, ephrinB2, and ephA4 expression, and the down-regulation of notch5 and notch6. In contrast, the expression of other genes, including mesp-a and papc, in the anterior of somite primordia, and the oscillating expression of deltaC and deltaD in the PSM appear normal. Nevertheless, this expression is apparently insufficient for the maturation of the presumptive somites to proceed to the stage when boundary formation occurs or for the maintenance of anterior/posterior patterning. Mouse embryos that are compound null mutants for Foxc1 and the closely related Foxc2 have no morphological somites and show abnormal expression of Notch signaling pathway genes in the anterior PSM. Therefore, zebrafish foxc1a plays an essential and conserved role in somite formation, regulating both the expression of paraxis and the A/P patterning of somite primordia.

FGF signaling controls somite boundary position and regulates segmentation clock control of spatiotemporal Hox gene activation

Vertebrate segmentation requires a molecular oscillator, the segmentation clock, acting in presomitic mesoderm (PSM) cells to set the pace at which segmental boundaries are laid down. However, the signals that position each boundary remain unclear. Here, we report that FGF8 which is expressed in the posterior PSM, generates a moving wavefront at which level both segment boundary position and axial identity become determined. Furthermore, by manipulating boundary position in the chick embryo, we show that Hox gene expression is maintained in the appropriately numbered somite rather than at an absolute axial position. These results implicate FGF8 in ensuring tight coordination of the segmentation process and spatiotemporal Hox gene activation.

Segmentation and somitogenesis derived from phase dynamics in growing oscillatory media

The formation of spatially repetitive structures along the growth axis of a developing embryo is a common theme in developmental biology. Here we apply the novel flow-distributed oscillator (FDO) mechanism of wave pattern formation to the problem of axial segmentation in general and to somitogenesis in particular. We argue that the conditions for formation of FDO waves are satisfied during somitogenesis in the chick and mouse and that the waves of gene expression observed in these species arise from phase dynamics in a growing oscillatory medium. We substantiate this claim by showing that the FDO mechanism allows the waves to be mimicked by an inorganic experiment and that it predicts a wavelength that coincides with that observed experimentally. To see whether the FDO mechanism is compatible with other aspects of somitogenesis, we construct an FDO-based model of somitogenesis and successfully test it against a number of experimental observations, including the effect of heat shock. Our analysis provides a rigorous physical basis for the hypothesis that the phase dynamics of a segmental clock controls important stages of segmentation during somitogenesis in the chick and mouse as well as in other organisms that undergo segmentation during their axial growth.