Spatial gradients of protein-level time delays set the pace of the traveling segmentation clock waves

DeltaC and DeltaD ligands play different roles in the segmentation clock dynamics

The vertebrate segmentation clock drives periodic somite segmentation during embryonic development. Her1 and Her7 clock proteins generate oscillatory expression of their own genes as well as that of deltaC in zebrafish. In turn, DeltaC and DeltaD ligands activate Notch signaling, which then activates transcription of clock genes in neighboring cells. While DeltaC and DeltaD proteins form homo- and heterodimers, only DeltaC-containing oscillatory dimers were expected to be functional. To investigate the contributions of DeltaC and DeltaD proteins on the transcription of her1 and her7 segmentation clock genes, we counted their transcripts by performing single molecule fluorescent in situ hybridization imaging in different genetic backgrounds of zebrafish embryos. Surprisingly, we found that DeltaD homodimers are also functional. We further found that Notch signaling promotes transcription of both deltaC and deltaD genes, thereby creating a previously unnoticed positive feedback loop. Our computational model highlighted the intriguing differential roles of DeltaC and DeltaD dimers on the clock synchronization and transcript numbers, respectively. We anticipate that a mechanistic understanding of the Notch signaling pathway will not only shed light on the mechanism driving robust somite segmentation but also inspire similar quantitative studies in other tissues and organs.

Cell-autonomous timing drives the vertebrate segmentation clock's wave pattern

Rhythmic and sequential segmentation of the growing vertebrate body relies on the segmentation clock, a multi-cellular oscillating genetic network. The clock is visible as tissue-level kinematic waves of gene expression that travel through the presomitic mesoderm (PSM) and arrest at the position of each forming segment. Here, we test how this hallmark wave pattern is driven by culturing single maturing PSM cells. We compare their cell-autonomous oscillatory and arrest dynamics to those we observe in the embryo at cellular resolution, finding similarity in the relative slowing of oscillations and arrest in concert with differentiation. This shows that cell-extrinsic signals are not required by the cells to instruct the developmental program underlying the wave pattern. We show that a cell-autonomous timing activity initiates during cell exit from the tailbud, then runs down in the anterior-ward cell flow in the PSM, thereby using elapsed time to provide positional information to the clock. Exogenous FGF lengthens the duration of the cell-intrinsic timer, indicating extrinsic factors in the embryo may regulate the segmentation clock via the timer. In sum, our work suggests that a noisy cell-autonomous, intrinsic timer drives the slowing and arrest of oscillations underlying the wave pattern, while extrinsic factors in the embryo tune this timer's duration and precision. This is a new insight into the balance of cell-intrinsic and -extrinsic mechanisms driving tissue patterning in development.

Cellular and molecular control of vertebrate somitogenesis

Segmentation is a fundamental feature of the vertebrate body plan. This metameric organization is first implemented by somitogenesis in the early embryo, when paired epithelial blocks called somites are rhythmically formed to flank the neural tube. Recent advances in in vitro models have offered new opportunities to elucidate the mechanisms that underlie somitogenesis. Notably, models derived from human pluripotent stem cells introduced an efficient proxy for studying this process during human development. In this Review, we summarize the current understanding of somitogenesis gained from both in vivo studies and in vitro studies. We deconstruct the spatiotemporal dynamics of somitogenesis into four distinct modules: dynamic events in the presomitic mesoderm, segmental determination, somite anteroposterior polarity patterning, and epithelial morphogenesis. We first focus on the segmentation clock, as well as signalling and metabolic gradients along the tissue, before discussing the clock and wavefront and other models that account for segmental determination. We then detail the molecular and cellular mechanisms of anteroposterior polarity patterning and somite epithelialization.

Ripply suppresses Tbx6 to induce dynamic-to-static conversion in somite segmentation

The metameric pattern of somites is created based on oscillatory expression of clock genes in presomitic mesoderm. However, the mechanism for converting the dynamic oscillation to a static pattern of somites is still unclear. Here, we provide evidence that Ripply/Tbx6 machinery is a key regulator of this conversion. Ripply1/Ripply2-mediated removal of Tbx6 protein defines somite boundary and also leads to cessation of clock gene expression in zebrafish embryos. On the other hand, activation of ripply1/ripply2 mRNA and protein expression is periodically regulated by clock oscillation in conjunction with an Erk signaling gradient. Whereas Ripply protein decreases rapidly in embryos, Ripply-triggered Tbx6 suppression persists long enough to complete somite boundary formation. Mathematical modeling shows that a molecular network based on results of this study can reproduce dynamic-to-static conversion in somitogenesis. Furthermore, simulations with this model suggest that sustained suppression of Tbx6 caused by Ripply is crucial in this conversion.

Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation

Biological time keeping, or the duration and tempo at which biological processes occur, is a phenomenon that drives dynamic molecular and morphological changes that manifest throughout many facets of life. In some cases, the molecular mechanisms regulating the timing of biological transitions are driven by genetic oscillations, or periodic increases and decreases in expression of genes described collectively as a "molecular clock." In vertebrate animals, molecular clocks play a crucial role in fundamental patterning and cell differentiation processes throughout development. For example, during early vertebrate embryogenesis, the segmentation clock regulates the patterning of the embryonic mesoderm into segmented blocks of tissue called somites, which later give rise to axial skeletal muscle and vertebrae. Segmentation clock oscillations are characterized by rapid cycles of mRNA and protein expression. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short-lived. Faithful, rhythmic, genetic oscillations are sustained by precise regulation at many levels, including post-transcriptional regulation, and such mechanisms are essential for proper vertebrate development. This article is categorized under: RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Regulation.

Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans

Oscillatory and sequential processes have been implicated in the spatial patterning of many embryonic tissues. For example, molecular clocks delimit segmental boundaries in vertebrates and insects and mediate lateral root formation in plants, whereas sequential gene activities are involved in the specification of regional identities of insect neuroblasts, vertebrate neural tube, vertebrate limb, and insect and vertebrate body axes. These processes take place in various tissues and organisms, and, hence, raise the question of what common themes and strategies they share. In this article, we review 2 processes that rely on the spatial regulation of periodic and sequential gene activities: segmentation and regionalization of the anterior-posterior (AP) axis of animal body plans. We study these processes in species that belong to 2 different phyla: vertebrates and insects. By contrasting 2 different processes (segmentation and regionalization) in species that belong to 2 distantly related phyla (arthropods and vertebrates), we elucidate the deep logic of patterning by oscillatory and sequential gene activities. Furthermore, in some of these organisms (e.g., the fruit fly Drosophila), a mode of AP patterning has evolved that seems not to overtly rely on oscillations or sequential gene activities, providing an opportunity to study the evolution of pattern formation mechanisms.

Time and space in segmentation

Arthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include: (i) the mechanistic origins of spatial organization within the segment addition zone (SAZ); (ii) the mechanistic origins of segment polarization; (iii) the mechanistic origins of axial variation; and (iv) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an 'oscillator', a 'switch' and up to three 'timers', successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarizing oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.

Muscle defects due to perturbed somite segmentation contribute to late adult scoliosis

Scoliosis is an abnormal bending of the body axis. Truncated vertebrae or a debilitated ability to control the musculature in the back can cause this condition, but in most cases the causative reason for scoliosis is unknown (idiopathic). Using mutants for somite clock genes with mild defects in the vertebral column, we here show that early defects in somitogenesis are not overcome during development and have long lasting and profound consequences for muscle fiber organization, structure and whole muscle volume. These mutants present only mild alterations in the vertebral column, and muscle shortcomings are uncoupled from skeletal defects. None of the mutants presents an overt musculoskeletal phenotype at larval or early adult stages, presumably due to compensatory growth mechanisms. Scoliosis becomes only apparent during aging. We conclude that adult degenerative scoliosis is due to disturbed crosstalk between vertebrae and muscles during early development, resulting in subsequent adult muscle weakness and bending of the body axis.

Segmentation clock dynamics is strongly synchronized in the forming somite

During vertebrate somitogenesis an inherent segmentation clock coordinates the spatiotemporal signaling to generate segmented structures that pattern the body axis. Using our experimental and quantitative approach, we study the cell movements and the genetic oscillations of her1 expression level at single-cell resolution simultaneously and scale up to the entire pre-somitic mesoderm (PSM) tissue. From the experimentally determined phases of PSM cellular oscillators, we deduced an in vivo frequency profile gradient along the anterior-posterior PSM axis and inferred precise mathematical relations between spatial cell-level period and tissue-level somitogenesis period. We also confirmed a gradient in the relative velocities of cellular oscillators along the axis. The phase order parameter within an ensemble of oscillators revealed the degree of synchronization in the tailbud and the posterior PSM being only partial, whereas synchronization can be almost complete in the presumptive somite region but with temporal oscillations. Collectively, the degree of synchronization itself, possibly regulated by cell movement and the synchronized temporal phase of the transiently expressed clock protein Her1, can be an additional control mechanism for making precise somite boundaries.

Somite boundary determination in normal and clock-less vertebrate embryos

Vertebrate segments called somites are generated by periodic segmentation of the presomitic mesoderm (PSM). In the most accepted theoretical model for somite segmentation, the clock and wavefront (CW) model, a clock that ticks to determine particular timings and a wavefront that moves posteriorly are presented in the PSM, and somite positions are determined when the clock meets the posteriorly moving wavefront somewhere in the PSM. Over the last two decades, it has been revealed that the molecular mechanism of the clock and wavefront in vertebrates is based on clock genes including Hes family transcription factors and Notch effectors that oscillate within the PSM to determine particular timings and fibroblast growth factor (FGF) gradients, acting as the posteriorly moving wavefront to determine the position of somite segmentation. A clock-less condition in the CW model was predicted to form no somites; however, irregularly sized somites were still formed in mice and zebrafish, suggesting that this was one of the limitations of the CW model. Recently, we performed interdisciplinary research of experimental and theoretical biological studies and revealed the mechanisms of somite boundary determination in normal and clock-less conditions by characterization of the FGF/extracellular signal-regulated kinase (ERK) activity dynamics. Since features of the molecular clock have already been described in-depth in several reviews, we summarized recent findings regarding the role of FGF/ERK signaling in somite boundary formation and described our current understanding of how FGF/ERK signaling contributes to somitogenesis in normal and clock-less conditions in this review.

Patterning via local cell-cell interactions in developing systems

Spatial patterning during embryonic development emerges from the differentiation of progenitor cells that share the same genetic program. One of the main challenges in systems biology is to understand the relationship between gene network and patterning, especially how the cells communicate to coordinate their differentiation. This review aims to describe the principles of pattern formation from local cell-cell interactions mediated by the Notch signalling pathway. Notch mediates signalling via direct cell-cell contact and regulates cell fate decisions in many tissues during embryonic development. Here, I will describe the patterning mechanisms via different Notch ligands and the critical role of Notch oscillations during the segmentation of the vertebrate body, brain development, and blood vessel formation.

Noise in the Vertebrate Segmentation Clock Is Boosted by Time Delays but Tamed by Notch Signaling

Taming cell-to-cell variability in gene expression is critical for precise pattern formation during embryonic development. To investigate the source and buffering mechanism of expression variability, we studied a biological clock, the vertebrate segmentation clock, controlling the precise spatiotemporal patterning of the vertebral column. By counting single transcripts of segmentation clock genes in zebrafish, we show that clock genes have low RNA amplitudes and expression variability is primarily driven by gene extrinsic sources, which is suppressed by Notch signaling. We further show that expression noise surprisingly increases from the posterior progenitor zone to the anterior segmentation and differentiation zone. Our computational model reproduces the spatial noise profile by incorporating spatially increasing time delays in gene expression. Our results, suggesting that expression variability is controlled by the balance of time delays and cell signaling in a vertebrate tissue, will shed light on the accuracy of natural clocks in multi-cellular systems and inspire engineering of robust synthetic oscillators.

Intrinsic noise, Delta-Notch signalling and delayed reactions promote sustained, coherent, synchronized oscillations in the presomitic mesoderm

Using a stochastic individual-based modelling approach, we examine the role that Delta-Notch signalling plays in the regulation of a robust and reliable somite segmentation clock. We find that not only can Delta-Notch signalling synchronize noisy cycles of gene expression in adjacent cells in the presomitic mesoderm (as is known), but it can also amplify and increase the coherence of these cycles. We examine some of the shortcomings of deterministic approaches to modelling these cycles and demonstrate how intrinsic noise can play an active role in promoting sustained oscillations, giving rise to noise-induced quasi-cycles. Finally, we explore how translational/transcriptional delays can result in the cycles in neighbouring cells oscillating in anti-phase and we study how this effect relates to the propagation of noise-induced stochastic waves.

Regulatory Network of the Scoliosis-Associated Genes Establishes Rostrocaudal Patterning of Somites in Zebrafish

Gene regulatory networks govern pattern formation and differentiation during embryonic development. Segmentation of somites, precursors of the vertebral column among other tissues, is jointly controlled by temporal signals from the segmentation clock and spatial signals from morphogen gradients. To explore how these temporal and spatial signals are integrated, we combined time-controlled genetic perturbation experiments with computational modeling to reconstruct the core segmentation network in zebrafish. We found that Mesp family transcription factors link the temporal information of the segmentation clock with the spatial action of the fibroblast growth factor signaling gradient to establish rostrocaudal (head to tail) polarity of segmented somites. We further showed that cells gradually commit to patterning by the action of different genes at different spatiotemporal positions. Our study provides a blueprint of the zebrafish segmentation network, which includes evolutionarily conserved genes that are associated with the birth defect congenital scoliosis in humans.

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A core network establishes rostrocaudal polarity of segmented somites in zebrafish

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mesp genes link the segmentation clock with the FGF signaling gradient

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Gradual patterning is done by the action of different genes at different positions

Size-reduced embryos reveal a gradient scaling-based mechanism for zebrafish somite formation

Little is known about how the sizes of animal tissues are controlled. A prominent example is somite size, which varies widely both within an individual and across species. Despite intense study of the segmentation clock governing the timing of somite generation, how it relates to somite size is poorly understood. Here, we examine somite scaling and find that somite size at specification scales with the length of the presomitic mesoderm (PSM) despite considerable variation in PSM length across developmental stages and in surgically size-reduced embryos. Measurement of clock period, axis elongation speed and clock gene expression patterns demonstrate that existing models fail to explain scaling. We posit a 'clock and scaled gradient' model, in which somite boundaries are set by a dynamically scaling signaling gradient across the PSM. Our model not only explains existing data, but also makes a unique prediction that we confirm experimentally - the formation of periodic 'echoes' in somite size following perturbation of the size of one somite. Our findings demonstrate that gradient scaling plays a central role in both progression and size control of somitogenesis.

Travelling waves in somitogenesis: Collective cellular properties emerge from time-delayed juxtacrine oscillation coupling

The sculpturing of the vertebrate body plan into segments begins with the sequential formation of somites in the presomitic mesoderm (PSM). The rhythmicity of this process is controlled by travelling waves of gene expression. These kinetic waves emerge from coupled cellular oscillators and sweep across the PSM. In zebrafish, the oscillations are driven by autorepression of her genes and are synchronized via Notch signalling. Mathematical modelling has played an important role in explaining how collective properties emerge from the molecular interactions. Increasingly more quantitative experimental data permits the validation of those mathematical models, yet leads to increasingly more complex model formulations that hamper an intuitive understanding of the underlying mechanisms. Here, we review previous efforts, and design a mechanistic model of the her1 oscillator, which represents the experimentally viable her7;hes6 double mutant. This genetically simplified system is ideally suited to conceptually recapitulate oscillatory entrainment and travelling wave formation, and to highlight open questions. It shows that three key parameters, the autorepression delay, the juxtacrine coupling delay, and the coupling strength, are sufficient to understand the emergence of the collective period, the collective amplitude, and the synchronization of neighbouring Her1 oscillators. Moreover, two spatiotemporal time delay gradients, in the autorepression and in the juxtacrine signalling, are required to explain the collective oscillatory dynamics and synchrony of PSM cells. The highlighted developmental principles likely apply more generally to other developmental processes, including neurogenesis and angiogenesis.

A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila

Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, such as the vinegar fly Drosophila melanogaster, determine all segments simultaneously through a hierarchical cascade of gene regulation. Gap genes constitute the first layer of the Drosophila segmentation gene hierarchy, downstream of maternal gradients such as that of Caudal (Cad). We use data-driven mathematical modelling and phase space analysis to show that shifting gap domains in the posterior half of the Drosophila embryo are an emergent property of a robust damped oscillator mechanism, suggesting that the regulatory dynamics underlying long- and short-germband segmentation are much more similar than previously thought. In Tribolium, Cad has been proposed to modulate the frequency of the segmentation oscillator. Surprisingly, our simulations and experiments show that the shift rate of posterior gap domains is independent of maternal Cad levels in Drosophila. Our results suggest a novel evolutionary scenario for the short- to long-germband transition and help explain why this transition occurred convergently multiple times during the radiation of the holometabolan insects.

Different insect species exhibit one of two distinct modes of determining their body segments (known as segmentation) during development: they either use a molecular oscillator to position segments sequentially, or they generate segments simultaneously through a hierarchical gene-regulatory cascade. The sequential mode is ancestral, while the simultaneous mode has been derived from it independently several times during evolution. In this paper, we present evidence suggesting that simultaneous segmentation also involves an oscillator in the posterior end of the embryo of the vinegar fly, Drosophila melanogaster. This surprising result indicates that both modes of segment determination are much more similar than previously thought. Such similarity provides an important step towards our understanding of the frequent evolutionary transitions observed between sequential and simultaneous segmentation.

ES cell-derived presomitic mesoderm-like tissues for analysis of synchronized oscillations in the segmentation clock

Somites are periodically formed by segmentation of the anterior parts of the presomitic mesoderm (PSM). In the mouse embryo, this periodicity is controlled by the segmentation clock gene Hes7, which exhibits wave-like oscillatory expression in the PSM. Despite intensive studies, the exact mechanism of such synchronous oscillatory dynamics of Hes7 expression still remains to be analyzed. Detailed analysis of the segmentation clock has been hampered because it requires the use of live embryos, and establishment of an in vitro culture system would facilitate such analyses. Here, we established a simple and efficient method to generate mouse ES cell-derived PSM-like tissues, in which Hes7 expression oscillates like traveling waves. In these tissues, Hes7 oscillation is synchronized between neighboring cells, and the posterior-anterior axis is self-organized as the central-peripheral axis. This method is applicable to chemical-library screening and will facilitate the analysis of the molecular nature of the segmentation clock.

Recent advances in understanding vertebrate segmentation

Segmentation is the partitioning of the body axis into a series of repeating units or segments. This widespread body plan is found in annelids, arthropods, and chordates, showing it to be a successful developmental strategy for growing and generating diverse morphology and anatomy. Segmentation has been extensively studied over the years. Forty years ago, Cooke and Zeeman published the Clock and Wavefront model, creating a theoretical framework of how developing cells could acquire and keep temporal and spatial information in order to generate a segmented pattern. Twenty years later, in 1997, Palmeirim and co-workers found the first clock gene whose oscillatory expression pattern fitted within Cooke and Zeeman's model. Currently, in 2017, new experimental techniques, such as new ex vivo experimental models, real-time imaging of gene expression, live single cell tracking, and simplified transgenics approaches, are revealing some of the fine details of the molecular processes underlying the inner workings of the segmentation mechanisms, bringing new insights into this fundamental process. Here we review and discuss new emerging views that further our understanding of the vertebrate segmentation clock, with a particular emphasis on recent publications that challenge and/or complement the currently accepted Clock and Wavefront model.

Modeling the Notch Response

NOTCH signaling regulates developmental processes in all tissues and all organisms across the animal kingdom. It is often involved in coordinating the differentiation of neighboring cells into different cell types. As our knowledge on the structural, molecular and cellular properties of the NOTCH pathway expands, there is a greater need for quantitative methodologies to get a better understanding of the processes controlled by NOTCH signaling. In recent years, theoretical and computational approaches to NOTCH signaling and NOTCH mediated patterning are gaining popularity. Mathematical models of NOTCH mediated patterning provide insight into complex and counterintuitive behaviors and can help generate predictions that can guide experiments. In this chapter, we review the recent advances in modeling NOTCH mediated patterning processes. We discuss new modeling approaches to lateral inhibition patterning that take into account cis-interactions between NOTCH receptors and ligands, signaling through long cellular protrusions, cell division processes, and coupling to external signals. We also describe models of somitogenesis, where NOTCH signaling is used for synchronizing cellular oscillations. We then discuss modeling approaches that consider the effect of cell morphology on NOTCH signaling and NOTCH mediated patterning. Finally, we consider models of boundary formation and how they are influenced by the combinatorial action of multiple ligands. Together, these topics cover the main advances in the field of modeling the NOTCH response.

Differential interactions between Notch and ID factors control neurogenesis by modulating Hes factor autoregulation

During embryonic and adult neurogenesis, neural stem cells (NSCs) generate the correct number and types of neurons in a temporospatial fashion. Control of NSC activity and fate is crucial for brain formation and homeostasis. Neurogenesis in the embryonic and adult brain differ considerably, but Notch signaling and inhibitor of DNA-binding (ID) factors are pivotal in both. Notch and ID factors regulate NSC maintenance; however, it has been difficult to evaluate how these pathways potentially interact. Here, we combined mathematical modeling with analysis of single-cell transcriptomic data to elucidate unforeseen interactions between the Notch and ID factor pathways. During brain development, Notch signaling dominates and directly regulates Id4 expression, preventing other ID factors from inducing NSC quiescence. Conversely, during adult neurogenesis, Notch signaling and Id2/3 regulate neurogenesis in a complementary manner and ID factors can induce NSC maintenance and quiescence in the absence of Notch. Our analyses unveil key molecular interactions underlying NSC maintenance and mechanistic differences between embryonic and adult neurogenesis. Similar Notch and ID factor interactions may be crucial in other stem cell systems.

Summary: Computational analysis of transcriptome data from neural stem cells reveals key differences in the synergistic interactions between Notch and inhibitor of DNA-binding factors during embryonic and adult neurogenesis.

Pnrc2 regulates 3'UTR-mediated decay of segmentation clock-associated transcripts during zebrafish segmentation

Vertebrate segmentation is controlled by the segmentation clock, a molecular oscillator that regulates gene expression and cycles rapidly. The expression of many genes oscillates during segmentation, including hairy/Enhancer of split-related (her or Hes) genes, which encode transcriptional repressors that auto-inhibit their own expression, and deltaC (dlc), which encodes a Notch ligand. We previously identified the tortuga (tor) locus in a zebrafish forward genetic screen for genes involved in cyclic transcript regulation and showed that cyclic transcripts accumulate post-splicing in tor mutants. Here we show that cyclic mRNA accumulation in tor mutants is due to loss of pnrc2, which encodes a proline-rich nuclear receptor co-activator implicated in mRNA decay. Using an inducible in vivo reporter system to analyze transcript stability, we find that the her1 3'UTR confers Pnrc2-dependent instability to a heterologous transcript. her1 mRNA decay is Dicer-independent and likely employs a Pnrc2-Upf1-containing mRNA decay complex. Surprisingly, despite accumulation of cyclic transcripts in pnrc2-deficient embryos, we find that cyclic protein is expressed normally. Overall, we show that Pnrc2 promotes 3'UTR-mediated decay of developmentally-regulated segmentation clock transcripts and we uncover an additional post-transcriptional regulatory layer that ensures oscillatory protein expression in the absence of cyclic mRNA decay.

The kinetics in mathematical models on segmentation clock genes in zebrafish

Somitogenesis is the process for the development of somites in vertebrate embryos. This process is timely regulated by synchronous oscillatory expression of the segmentation clock genes. Mathematical models expressed by delay equations or ODEs have been proposed to depict the kinetics of these genes in interacting cells. Through mathematical analysis, we investigate the parameter regimes for synchronous oscillations and oscillation-arrested in an ODE model and a model with transcriptional and translational delays, both with Michaelis-Menten type degradations. Comparisons between these regimes for the two models are made. The delay model has larger capacity to accommodate synchronous oscillations. Based on the analysis and numerical computations extended from the analysis, we explore how the periods and amplitudes of the oscillations vary with the degradation rates, synthesis rates, and coupling strength. For typical parameter values, the period and amplitude increase as some synthesis rate or the coupling strength increases in the ODE model. Such variational properties of oscillations depend also on the magnitudes of time delays in delay model. We also illustrate the difference between the dynamics in systems modeled with linear degradation and the ones in systems with Michaelis-Menten type reactions for the degradation. The chief concerns are the connections between the dynamics in these models and the mechanism for the segmentation clocks, and the pertinence of mathematical modeling on somitogenesis in zebrafish.

Persistence, period and precision of autonomous cellular oscillators from the zebrafish segmentation clock

In vertebrate development, the sequential and rhythmic segmentation of the body axis is regulated by a “segmentation clock”. This clock is comprised of a population of coordinated oscillating cells that together produce rhythmic gene expression patterns in the embryo. Whether individual cells autonomously maintain oscillations, or whether oscillations depend on signals from neighboring cells is unknown. Using a transgenic zebrafish reporter line for the cyclic transcription factor Her1, we recorded single tailbud cells in vitro. We demonstrate that individual cells can behave as autonomous cellular oscillators. We described the observed variability in cell behavior using a theory of generic oscillators with correlated noise. Single cells have longer periods and lower precision than the tissue, highlighting the role of collective processes in the segmentation clock. Our work reveals a population of cells from the zebrafish segmentation clock that behave as self-sustained, autonomous oscillators with distinctive noisy dynamics.

DOI:http://dx.doi.org/10.7554/eLife.08438.001

The timing and pattern of gene activity in cells can be very important. For example, precise gene activity patterns in 24-hour circadian clocks help to set daily cycles of rest and activity in organisms. In such scenarios, cells often communicate with each other to coordinate the activity of their genes. To fully understand how the behavior of the population emerges, scientists must first understand the gene activity patterns in individual cells.

Rhythmic gene activity is essential for the spinal column to form in fish and other vertebrate embryos. A group of cells that switch genes on/off in a coordinated pattern act like a clock to regulate the timing of the various steps in the process of backbone formation. However, it is not clear if each cell is able to maintain a rhythm of gene expression on their own, or whether they rely on messages from neighboring cells to achieve it.

Now, Webb et al. use time-lapse videos of individual cells isolated from the tail of zebrafish embryos to show that each cell can maintain a pattern of rhythmic activity in a gene called Her1. In the experiments, individual cells were removed from zebrafish and placed under a microscope to record and track the activity of Her1 over time using fluorescent proteins. These experiments show that each cell is able to maintain a rhythmic pattern of Her1 expression on its own.

Webb et al. then compared the Her1 activity patterns in individual cells with the Her1 patterns present in a larger piece of zebrafish tissue. The experiments showed that the rhythms in the individual cells are slower and less precise in their timing than in the tissue. This suggests that groups of cells must work together to create the synchronized rhythms of gene expression with the right precision and timing needed for the spinal column to be patterned correctly.

In the future, further experiment with these cells will allow researchers to investigate the genetic basis of the rhythms in single cells, and find out how individual cells work together with their neighbors to allow tissues to work properly.

DOI:http://dx.doi.org/10.7554/eLife.08438.002

Dynamics of the slowing segmentation clock reveal alternating two-segment periodicity

The formation of reiterated somites along the vertebrate body axis is controlled by the segmentation clock, a molecular oscillator expressed within presomitic mesoderm (PSM) cells. Although PSM cells oscillate autonomously, they coordinate with neighboring cells to generate a sweeping wave of cyclic gene expression through the PSM that has a periodicity equal to that of somite formation. The velocity of each wave slows as it moves anteriorly through the PSM, although the dynamics of clock slowing have not been well characterized. Here, we investigate segmentation clock dynamics in the anterior PSM in developing zebrafish embryos using an in vivo clock reporter, her1:her1-venus. The her1:her1-venus reporter has single-cell resolution, allowing us to follow segmentation clock oscillations in individual cells in real-time. By retrospectively tracking oscillations of future somite boundary cells, we find that clock reporter signal increases in anterior PSM cells and that the periodicity of reporter oscillations slows to about ∼1.5 times the periodicity in posterior PSM cells. This gradual slowing of the clock in the anterior PSM creates peaks of clock expression that are separated at a two-segment periodicity both spatially and temporally, a phenomenon we observe in single cells and in tissue-wide analyses. These results differ from previous predictions that clock oscillations stop or are stabilized in the anterior PSM. Instead, PSM cells oscillate until they incorporate into somites. Our findings suggest that the segmentation clock may signal somite formation using a phase gradient with a two-somite periodicity.