temporal-ordering-dynamic-expression-data-from-detailed-spatial

Temporal Ordering of Dynamic Expression Data from Detailed Spatial Expression Maps

During somitogenesis, pairs of epithelial somites form in a progressive manner, budding off from the anterior end of the pre-somitic mesoderm (PSM) with a ...

University of Dundee

During somitogenesis an oscillatory mechanism termed the "segmentation" clock generates periodic waves of gene expression, which translate into the periodic spatial pattern manifest as somites. The dynamic expression of the clock genes shares the same periodicity as somitogenesis. Notch signaling is believed to play a role in the segmentation clock mechanism. The paper by Hirata et al.(1) identifies a biological clock in cultured cells that is dependent upon the Notch target gene Hes1, and which shows a periodicity similar to that of the segmentation clock. This finding opens the possibility that the same oscillator mechanism might also operate in other tissues or cell types.

A Hes1-based oscillator in cultured cells and its potential implications for the segmentation clock.

Segmentation of the vertebrate body axis is initiated early in development with the sequential formation of somites. Somitogenesis is temporally regulated by a molecular oscillator, the segmentation clock, which acts within presomitic mesoderm (PSM) cells to drive periodic expression of the cyclic genes. We have investigated the kinetics of the progression of cycling gene expression along the PSM. Here we show that c-hairy1 and c-hairy2 mRNA expression traverses the PSM in an entirely progressive manner and that both these genes and c-Lfng maintain a similar anterior limit of expression during each cycle. However, some differences are seen regarding both the onset of a new oscillation of these genes and the duration of their expression in the caudal PSM. We also investigated whether oscillating cyclic gene expression in the PSM is entirely cell autonomous. We find that while small PSM explants are still able to maintain their oscillation schedule, once they are dissociated, PSM cells are no longer able to maintain synchronous oscillations. The results imply that cell communication or a community effect is essential for the normal pattern of cyclic gene expression in these cells.

Synchronised cycling gene oscillations in presomitic mesoderm cells require cell-cell contact.

Temporal control is considered the fourth dimension in embryonic development and it sets the pace to attain the correct molecular patterning of the developing embryo. In this chapter we review one of the best-studied time dependent events in embryogenesis, which is the formation ofsomites. Somites are the basis of the future segmented framework of the vertebrate adult body and their reiterated appearance during the early stages of embryo development establishes the proper temporal and physical template from where other structures will develop and consequently shape the segmentation pattern of the embryo. Several models have been proposed over the last few decades to explain the mechanism(s) regulating somite periodicity, but no molecular evidence seemed to back up any of the postulated models. Remarkably, in 1997 the first evidence that the formation of the somites depended on an intrinsic molecular clock was at last provided through the description of oscillating gene expression in the tissue from which somites are generated. Since then, a huge amount of data has been and continues to be provided that is gradually revealing the ever more complex molecular mechanism underlying this segmentation clock. We are also beginning to learn about embryonic structures other than the somites which exhibit oscillations of gene expression suggesting they too are dependent upon a segmentation-like clock. This is in itself the clearest evidence that there is still a long way to go before we unveil the myriad of molecular mechanisms that lead to the time control of embryonic development.

Development on time.

Somites are embryonic precursors of the ribs, vertebrae and certain dermis tissue. Somite formation is a periodic process regulated by a molecular clock which drives cyclic expression of a number of clock genes in the presomitic mesoderm. To date the mechanism regulating the period of clock gene oscillations is unknown. Here we show that chick homologues of the Wnt pathway genes that oscillate in mouse do not cycle across the chick presomitic mesoderm. Strikingly we find that modifying Wnt signalling changes the period of Notch driven oscillations in both mouse and chick but these oscillations continue. We propose that the Wnt pathway is a conserved mechanism that is involved in regulating the period of cyclic gene oscillations in the presomitic mesoderm.

Interfering with Wnt signalling alters the periodicity of the segmentation clock.

During vertebrate embryogenesis, somites are generated at regular intervals, the temporal and spatial periodicity of which is governed by a gradient of fibroblast growth factor (FGF) and/or Wnt signaling activity in the presomitic mesoderm (PSM) in conjunction with oscillations of gene expression of components of the Notch, Wnt and FGF signaling pathways.

Sprouty4, an FGF inhibitor, displays cyclic gene expression under the control of the notch segmentation clock in the mouse PSM.

Segmentation of the vertebrate body axis is initiated through somitogenesis, whereby epithelial somites bud off in pairs periodically from the rostral end of the unsegmented presomitic mesoderm (PSM). The periodicity of somitogenesis is governed by a molecular oscillator that drives periodic waves of clock gene expression caudo-rostrally through the PSM with a periodicity that matches somite formation. To date the clock genes comprise components of the Notch, Wnt, and FGF pathways. The literature contains controversial reports as to the absolute role(s) of Notch signalling during the process of somite formation. Recent data in the zebrafish have suggested that the only role of Notch signalling is to synchronise clock gene oscillations across the PSM and that somite formation can continue in the absence of Notch activity. However, it is not clear in the mouse if an FGF/Wnt-based oscillator is sufficient to generate segmented structures, such as the somites, in the absence of all Notch activity. We have investigated the requirement for Notch signalling in the mouse somitogenesis clock by analysing embryos carrying a mutation in different components of the Notch pathway, such as Lunatic fringe (Lfng), Hes7, Rbpj, and presenilin1/presenilin2 (Psen1/Psen2), and by pharmacological blocking of the Notch pathway. In contrast to the fish studies, we show that mouse embryos lacking all Notch activity do not show oscillatory activity, as evidenced by the absence of waves of clock gene expression across the PSM, and they do not develop somites. We propose that, at least in the mouse embryo, Notch activity is absolutely essential for the formation of a segmented body axis.

Notch is a critical component of the mouse somitogenesis oscillator and is essential for the formation of the somites.

Somites are formed progressively from the presomitic mesoderm (PSM) in a highly regulated process according to a strict periodicity driven by an oscillatory mechanism. The Notch and Wnt pathways are key components in the regulation of this somitic oscillator and data from Xenopus and zebrafish embryos indicate that the Notch-downstream target Nrarp participates in the regulation of both activities. We have analyzed Nrarp/nrarp-a expression in the PSM of chick, mouse and zebrafish embryos, and we show that it cycles in synchrony with other Notch regulated cyclic genes. In the mouse its transcription is both Wnt- and Notch-dependent, whereas in the chick and fish embryo it is simply Notch-dependent. Despite oscillating mRNA levels, Nrarp protein does not oscillate in the PSM. Finally, neither gain nor loss of Nrarp function interferes with the normal expression of Notch-related cyclic genes.

Cyclic Nrarp mRNA expression is regulated by the somitic oscillator but Nrarp protein levels do not oscillate.

Hensen's node of the chick embryo contains multipotent self-renewing progenitor cells that can contribute to either the floor plate or the notochord. Floor plate cells are a population of epithelial cells that lie at the ventral midline of the developing neural tube, whereas the notochord is a rod of axial mesoderm that lies directly beneath the floor plate. These two tissues serve as a source of a potent signalling morphogen, sonic hedgehog (Shh), which patterns the dorsoventral axis of the neural tube. We show, through both gain- and loss-of-function approaches, that Notch signalling promotes the contribution of chick axial progenitor cells to the floor plate and inhibits contribution to the notochord. Thus, we propose that Notch regulates the allocation of appropriate numbers of progenitor cells from Hensen's node of the chick embryo to the notochord and the floor plate.

Notch signalling regulates the contribution of progenitor cells from the chick Hensen's node to the floor plate and notochord.

The vertebrate segmentation clock is a molecular oscillator that regulates the periodicity of somite formation. Three signalling pathways have been proposed to underlie the molecular mechanism of the oscillator, namely the Notch, Wnt and Fgf pathways. Characterizing the roles and hierarchy of these three pathways in the oscillator mechanism is currently the focus of intense research. Recent publications report the first identification of a molecular mechanism involved in the regulation of the pace of this oscillator. We review these and other recent findings regarding the interaction between the three pathways in the oscillator mechanism that have significantly expanded our understanding of the segmentation clock.

The segmentation clock mechanism moves up a notch.

The most obvious manifestation of the existence of a segmented, or metameric, body plan in vertebrate embryos is seen during the formation of the somites. Somites are transient embryonic structures formed in a progressive manner from a nonsegmented mesoderm in a highly regulated process called somitogenesis. As development proceeds different compartments are formed within each somite and these progressively follow a variety of differentiation programs to form segmented organs, such as the different bones that make the axial skeleton, body skeletal muscles and part of the dermis. Transcription factors from the basic helix-loop-helix (bHLH) protein family have been described to be implicated in each of the processes involved in somite formation. bHLH proteins are a family of transcription factors characterized by the presence of a DNA binding domain and a dimerization motif that consists of a basic region adjacent to an amphipathic helix, a loop and a second amphipathic helix. In this chapter we will review a number of bHLH proteins known to play a role in somitogenesis.

BHLH proteins and their role in somitogenesis.

In the vertebrate embryo, tissue blocks called somites are laid down in head-to-tail succession, a process known as somitogenesis. Research into somitogenesis has been both experimental and mathematical. For zebrafish, there is experimental evidence for oscillatory gene expression in cells in the presomitic mesoderm (PSM) as well as evidence that Notch signalling synchronises the oscillations in neighbouring PSM cells. A biological mechanism has previously been proposed to explain these phenomena. Here we have converted this mechanism into a mathematical model of partial differential equations in which the nuclear and cytoplasmic diffusion of protein and mRNA molecules is explicitly considered. By performing simulations, we have found ranges of values for the model parameters (such as diffusion and degradation rates) that yield oscillatory dynamics within PSM cells and that enable Notch signalling to synchronise the oscillations in two touching cells. Our model contains a Hill coefficient that measures the co-operativity between two proteins (Her1, Her7) and three genes (her1, her7, deltaC) which they inhibit. This coefficient appears to be bounded below by the requirement for oscillations in individual cells and bounded above by the requirement for synchronisation. Consistent with experimental data and a previous spatially non-explicit mathematical model, we have found that signalling can increase the average level of Her1 protein. Biological pattern formation would be impossible without a certain robustness to variety in cell shape and size; our results possess such robustness. Our spatially-explicit modelling approach, together with new imaging technologies that can measure intracellular protein diffusion rates, is likely to yield significant new insight into somitogenesis and other biological processes.

A spatio-temporal model of Notch signalling in the zebrafish segmentation clock: conditions for synchronised oscillatory dynamics.

A segmented body plan is fundamental to all vertebrate species and this bestows both rigidity and flexibility on the body. Segmentation is initiated through the process of somitogenesis. This article aims to provide a broad and balanced cross-species overview of somitogenesis and to highlight the key molecular and cellular events involved in each stage of segmentation. We highlight where our understanding of this multifaceted process relies on strong experimental evidence as well as those aspects where our understanding still relies largely on models.

Somitogenesis.

Biofilm formation by the Gram-positive bacterium Bacillus subtilis is tightly controlled at the level of transcription. The biofilm contains specialised cell types that arise from controlled differentiation of the resident isogenic bacteria. DegU is a response regulator that controls several social behaviours exhibited by B. subtilis including swarming motility, biofilm formation and extracellular protease (exoprotease) production. Here, for the first time, we examine the prevalence and origin of exoprotease producing cells within the biofilm. This was accomplished using single cell analysis techniques including flow cytometry and fluorescence microscopy. We established that the number of exoprotease producing cells increases in prevalence as the biofilm matures. This is reflected by both an increase at the level of transcription and an increase in extracellular protease activity over time. We go on to demonstrate that exoprotease producing cells arise from more than one cell type; namely matrix producing and non-matrix producing cells. In toto these findings allow us to add exoprotease producing cells to the list of specialised cell types that are derived during B. subtilis biofilm formation and furthermore the data highlights the plasticity in the origin of differentiated cells.

The prevalence and origin of exoprotease producing cells in the Bacillus subtilis biofilm.

During somitogenesis, epithelial somites form from the pre-somitic mesoderm (PSM) in a periodic manner. This periodicity is regulated by a molecular oscillator, known as the 'segmentation clock', that is characterised by an oscillatory pattern of gene expression that sweeps the PSM in a caudal-rostral direction. Key components of the segmentation clock are intracellular components of the Notch, Wnt and FGF pathways, and it is widely accepted that intracellular negative-feedback loops regulate oscillatory gene expression. However, an open question in the field is how intracellular oscillations are coordinated, in the form of spatiotemporal waves of expression, across the PSM. In this study, we provide a potential mechanism for this process. We show at the mRNA level that the Notch1 receptor and Delta-like 1 (Dll1) ligand vary dynamically across the PSM of both chick and mouse. Remarkably, we also demonstrate similar dynamics at the protein level; hence, the pathway components that mediate intercellular coupling themselves exhibit oscillatory dynamics. Moreover, we quantify the dynamic expression patterns of Dll1 and Notch1, and show they are highly correlated with the expression patterns of two known clock components [Lfng mRNA and the activated form of the Notch receptor (cleaved Notch intracellular domain, NICD)]. Lastly, we show that Notch1 is a target of Notch signalling, whereas Dll1 is Wnt regulated. Regulation of Dll1 and Notch1 expression thus links the activity of Wnt and Notch, the two main signalling pathways driving the clock.

Spatiotemporal oscillations of Notch1, Dll1 and NICD are coordinated across the mouse PSM.

Notochord-derived Sonic Hedgehog (Shh) is essential for dorsoventral patterning of the overlying neural tube. Increasing concentration and duration of Shh signal induces progenitors to acquire progressively more ventral fates. We show that Notch signalling augments the response of neuroepithelial cells to Shh, leading to the induction of higher expression levels of the Shh target gene Ptch1 and subsequently induction of more ventral cell fates. Furthermore, we demonstrate that activated Notch1 leads to pronounced accumulation of Smoothened (Smo) within primary cilia and elevated levels of full-length Gli3. Finally, we show that Notch activity promotes longer primary cilia both in vitro and in vivo. Strikingly, these Notch-regulated effects are Shh independent. These data identify Notch signalling as a novel modulator of Shh signalling that acts mechanistically via regulation of ciliary localisation of key components of its transduction machinery.

A conserved role for Notch signaling in priming the cellular response to Shh through ciliary localisation of the key Shh transducer Smo.

Somitogenesis is regulated by a molecular oscillator that drives dynamic gene expression within the pre-somitic mesoderm. Previous mathematical models of the somitogenesis clock that invoke the mechanism of delayed negative feedback predict that its oscillation period depends on the sum of delays inherent to negative-feedback loops and inhibitor half-lives. We develop a mathematical model that explores the possibility that positive feedback also plays a role in determining the period of clock oscillations. The model predicts that increasing the half-life of the positive regulator, Notch intracellular domain (NICD), can lead to elevated NICD levels and an increase in the oscillation period. To test this hypothesis, we investigate a phenotype induced by various small molecule inhibitors in which the clock is slowed. We observe elevated levels and a prolonged half-life of NICD. Reducing NICD production rescues these effects. These data provide the first indication that tight control of the turnover of positive as well as negative regulators of the clock determines its periodicity.

Article	Year
A Hes1-based oscillator in cultured cells and its potential implications for the segmentation clock. BioEssays : news and reviews in molecular, cellular and developmental biology\| PubMed ID: 12596223	2003
Synchronised cycling gene oscillations in presomitic mesoderm cells require cell-cell contact. The International journal of developmental biology\| PubMed ID: 15906246	2005
Development on time. Advances in experimental medicine and biology\| PubMed ID: 18783172	2008
Interfering with Wnt signalling alters the periodicity of the segmentation clock. Developmental biology\| PubMed ID: 19272372	2009
Sprouty4, an FGF inhibitor, displays cyclic gene expression under the control of the notch segmentation clock in the mouse PSM. PloS one\| PubMed ID: 19440349	2009
Notch is a critical component of the mouse somitogenesis oscillator and is essential for the formation of the somites. PLoS genetics\| PubMed ID: 19779553	2009
Cyclic Nrarp mRNA expression is regulated by the somitic oscillator but Nrarp protein levels do not oscillate. Developmental dynamics : an official publication of the American Association of Anatomists\| PubMed ID: 19882724	2009
Notch signalling regulates the contribution of progenitor cells from the chick Hensen's node to the floor plate and notochord. Development (Cambridge, England)\| PubMed ID: 20110321	2010
The segmentation clock mechanism moves up a notch. Trends in cell biology\| PubMed ID: 20724159	2010
BHLH proteins and their role in somitogenesis. Advances in experimental medicine and biology\| PubMed ID: 21038774	2008
A spatio-temporal model of Notch signalling in the zebrafish segmentation clock: conditions for synchronised oscillatory dynamics. PloS one\| PubMed ID: 21386903	2011
Somitogenesis. Development (Cambridge, England)\| PubMed ID: 22736241	2012
The prevalence and origin of exoprotease producing cells in the Bacillus subtilis biofilm. Microbiology (Reading, England)\| PubMed ID: 24149708	2013
Spatiotemporal oscillations of Notch1, Dll1 and NICD are coordinated across the mouse PSM. Development (Cambridge, England)\| PubMed ID: 25468943	2014
A conserved role for Notch signaling in priming the cellular response to Shh through ciliary localisation of the key Shh transducer Smo. Development (Cambridge, England)\| PubMed ID: 25995356	2015
A balance of positive and negative regulators determines the pace of the segmentation clock. eLife\| PubMed ID: 26357015	2015

J. Kim Dale

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