Somitogenesis in Vertebrate Development


A segmented body plan is a conserved feature of all vertebrate species and is established early in embryonic development by the formation of somites, the precursors to the skeleton, musculature and dermis. These epithelialised structures are formed with a species‐specific periodicity during the process of somitogenesis. Gathering evidence suggests that somitogenesis is regulated by a molecular oscillator mechanism that, together with a morphogenic gradient, stipulates when and where somites form. Mutations in key molecular players in this mechanism have been closely linked to developmental disorders and segmental malformations. It is therefore of great medical interest to elucidate the regulatory mechanisms which govern this key developmental process, much of which is still not yet fully understood.

Key Concepts

  • A segmented body plan is a conserved feature of all vertebrate species.
  • Somitogenesis describes the periodic formation of somites, which is the first overt sign of segmentation to appear in the embryonic vertebrate body plan.
  • The temporal periodicity of somitogenesis is thought to be regulated by a molecular oscillator mechanism termed the segmentation clock.
  • There is emerging evidence to suggest a significant degree of conservation of the regulatory mechanisms governing somitogenesis in different vertebrate species.
  • Some particular disease states characterised by segmentation defects have been shown to result from mutation in key Notch‐regulated components of somitogenesis.
  • Many of the mechanisms thought to regulate somitogenesis and somite boundary formation appear to be highly reliant on the Notch signalling pathway.
  • There is a large degree of crosstalk between the Notch, Wnt and FGF signalling pathways that orchestrate somitogenesis.
  • Future advances in our understanding of the regulatory mechanisms governing somitogenesis rely on developing mathematical models and interdisciplinary approaches to direct and cooperate with biological investigation.

Keywords: vertebrate segmentation; molecular oscillations; clock; wavefront; Notch signalling; molecular crosstalk; mathematical modelling; somites

Figure 1. Somite maturation in the vertebrate embryo. In the newly formed somite, an epithelial layer of mesodermal cells surrounds a central lumen termed the somitocoel which contains loose mesenchyme cells. As the somite matures, the ventral epithelial cells disaggregate and together with the somitocoel, become the sclerotome. The remaining epithelial cells differentiate into the dermomyotome. SE, surface ectoderm; DRG, dorsal root ganglion; NC, notochord; FP, floor plate; NT, neural tube.
Figure 2. Phenotypes of spondylocostal dysostosis (SCD). The formation of hemi‐vertebrae (a) and fused ribs (b) together with shortening of the body axis and vertebral transformations are associated with the SCD phenotype. Mutations in key regulatory components of somitogenesis; Dll3 (Turnpenny et al., ), Mesp2 (Whittock et al., ), Lunatic fringe (Lfng) (Sparrow et al., ) and Hairy and Enhancer of Split 7 (Hes7) (Sparrow et al., ), have been linked to SCD (c) indicating that disruption of somite and boundary formation underlies this phenotype in these patients. Images are sourced from the indicated primary references. Dll3: Reproduced with permission form Turnpenny 2007 © John Wiley and Sons. Mesp2: Reproduced from Whittock 2004 © Elsevier. Lfng: Reproduced from Sparrow et al 2006 © Elsevier. Hes7: Reproduced from Sparrow et al 2010 © Nature Publishing Group.
Figure 3. The characterisation of the vertebrate segmentation clock oscillator. Waves of gene transcription from clock genes appear to originate in the tail‐bud of the pre‐somitic mesoderm (PSM) and progress caudo‐rostrally across this tissue with a periodicity which matches somite formation. The progress of these oscillations across this tissue is described in well‐characterised phases (a). Somite boundary formation occurs between phase 2 and 3 of the segmentation clock cycle. In chick, dissection of the PSM from neighbouring tissues to remove external cues and/or division of the PSM into multiple pieces does not prevent correctly timed coherent oscillations in clock gene expression indicating the cell autonomy of this process. In both chick and zebrafish, dissociation of PSM cells completely from their neighbours does not prevent oscillations but results in a loss of synchrony between cells (b).
Figure 4. The intracellular oscillations of the segmentation clock are governed predominantly by transient negative feedback loops. Trans‐activation of Notch signalling between adjacent cells initiates a series of cleavage events that liberate the intracellular portion of the Notch receptor (NICD). NICD associates with additional cofactors in the nucleus of the signal receiving cell to activate downstream target genes. Lfng acts to inhibit Notch signalling via post‐translational modification of Notch receptor while Hes7 binds as a dimer to the promoter sequences of Notch target genes, including its own promoter and prevents activation of transcription. However, both Lfng and Hes7 are actively and rapidly degraded allowing for the next wave of signalling. Therefore, the auto‐repression of Notch signalling is transient and leads to pulsatile transcription.
Figure 5. Sources of delay in the segmentation clock oscillation period. The total period of segmentation clock cycle is the sum of the time taken for the following identifiable processes: clock gene transcription, intron splicing, mRNA nuclear export, translation, nuclear import, protein complex assembly, DNA binding and protein/mRNA decay.
Figure 6. The wavefront activity of the PSM may control somite size. The wavefront activity of the PSM is thought to be established by opposing gradients of FGF/Wnt and retinoic acid (RA). The intersection of these gradients is termed the determination front and once cells become displaced rostral to that point in the PSM they can respond to the molecular oscillator and embark on their segmentation programme (a). Studies in the chick have shown that the position of the determination front and hence somite size can be altered by manipulation of FGF signalling such as with the FGFR inhibitor SU5402 (b) or an Fgf8 soaked bead (c).
Figure 7. The molecular cascade of somite boundary formation and morphological re‐segmentation of the sclerotome. Expression domains of key components of the segmentation machinery are indicated by colour coded bars in the PSM schematic shown in (a) and (b). Expression of Mesp2 (magenta) is promoted in the rostral PSM (S‐1) by the cooperation of Notch activity (NICD; dark blue) and Tbx6 (green) (1). As the segmentation clock cycle progresses, Mesp2 actively downregulates its own transcription via inhibition of key transcriptional regulators MamL and Tbx6 and activation of the Notch signalling inhibitor Lfng (not shown). The Mesp2 expression domain is further refined by the action of transcriptional repressor Ripply1/2 (purple) (2). Notch activity is thereby restricted to the caudal half of the forming somite, while Mesp2 becomes restricted to the rostral half which establishes the subdivision of the somites. As somites begin to mature and differentiate, the sclerotome from the caudal half of one somite fuses with the rostral half of its neighbour to form the definitive vertebrae, in a process termed re‐segmentation.
Figure 8. Establishing anterior–posterior (AP) polarity of the body axis using the Hox gene code. Vertebrae have distinct morphologies depending on their location along the AP axis. Hox genes provide the basis for this specification. These genes are expressed in restricted domains along the axis. Different combinations of genes, referred to as the Hox code, expressed within different somites specify different vertebra characteristics. The Hox code underlying specification of each vertebra along the antero‐posterior body axis of the mouse is shown here. Reproduced with permission from Dr Robert A. Bone.


Aulehla A and Pourquié O (2010) Signaling gradients during paraxial mesoderm development. Cold Spring Harbor Perspectives in Biology 2 (2): a000869–a000869.

Bone RA et al. (2014) Spatiotemporal oscillations of Notch1, Dll1 and NICD are coordinated across the mouse PSM. Development (Cambridge, England) 141 (24): 4806–4816.

Bonev B , Stanley P and Papalopulu N (2012) MicroRNA‐9 Modulates Hes1 ultradian oscillations by forming a double‐negative feedback loop. Cell Reports 2 (1): 10–18.

Burke AC (2000) Hox genes and the global patterning of the somitic mesoderm. Current Topics in Developmental Biology 47: 155–181.

Carapuço M et al. (2005) Hox genes specify vertebral types in the presomitic mesoderm. Genes & Development 19 (18): 2116–2121.

Chapman G et al. (2011) Notch inhibition by the ligand DELTA‐LIKE 3 defines the mechanism of abnormal vertebral segmentation in spondylocostal dysostosis. Human Molecular Genetics 20 (5): 905–916.

Cole SE et al. (2002) Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis. Developmental Cell 3 (1): 75–84.

Cooke J and Zeeman EC (1976) A clock and wavefront model for control of the number of repeated structures during animal morphogenesis. Journal of Theoretical Biology 58 (2): 455–476.

Dale JK et al. (2003) Periodic Notch inhibition by Lunatic Fringe underlies the chick segmentation clock. Nature 421 (6920): 275–278.

Delaune EA et al. (2012) Single‐cell‐resolution imaging of the impact of Notch signaling and mitosis on segmentation clock dynamics. Developmental Cell 23 (5): 995–1005.

Dequéant M‐L et al. (2006) A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science (New York, N.Y.) 314 (5805): 1595–1598.

Dias AS et al. (2014) Somites without a clock. Science (New York, N.Y.) 343 (6172): 791–795.

Diez del Corral R et al. (2003) Opposing FGF and retinoid pathways control ventral neural pattern, neuronal differentiation, and segmentation during body axis extension. Neuron 40 (1): 65–79.

Ferjentsik Z et al. (2009) Notch is a critical component of the mouse somitogenesis oscillator and is essential for the formation of the somites CA Henry , ed.. PLoS Genetics 5 (9): e1000662.

Gajewski M et al. (2003) Anterior and posterior waves of cyclic her1 gene expression are differentially regulated in the presomitic mesoderm of zebrafish. Development (Cambridge, England) 130 (18): 4269–4278.

Gomez C et al. (2008) Control of segment number in vertebrate embryos. Nature 454 (7202): 335–339.

Gridley T and Zhang N (1998) Defects in somite formation in lunatic fringe‐deficient mice. Nature 394 (6691): 374–377.

Harima Y et al. (2013) Accelerating the tempo of the segmentation clock by reducing the number of introns in the Hes7 gene. Cell Reports 3 (1): 1–7.

Harima Y et al. (2014) The roles and mechanism of ultradian oscillatory expression of the mouse Hes genes. Seminars in Cell & Developmental Biology 34: 85–90.

Hoyle NP and Ish‐Horowicz D (2013) Transcript processing and export kinetics are rate‐limiting steps in expressing vertebrate segmentation clock genes. Proceedings of the National Academy of Sciences of the United States of America 110 (46): E4316–24.

Iimura T and Pourquié O (2006) Collinear activation of Hoxb genes during gastrulation is linked to mesoderm cell ingression. Nature 442 (7102): 568–571.

Johnson RL et al. (1998) Lunatic fringe is an essential mediator of somite segmentation and patterning. Nature 394 (6691): 377–381.

Kieny M , Mauger A and Sengel P (1972) Early regionalization of somitic mesoderm as studied by the development of axial skeleton of the chick embryo. Developmental Biology 28 (1): 142–161.

Krol AJ et al. (2011) Evolutionary plasticity of segmentation clock networks. Development (Cambridge, England) 138 (13): 2783–2792.

Lauschke VM et al. (2013) Scaling of embryonic patterning based on phase‐gradient encoding. Nature 493 (7430): 101–105.

Lewis J (2003) Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator. Current Biology: CB 13 (16): 1398–1408.

Maroto M et al. (2005) Synchronised cycling gene oscillations in presomitic mesoderm cells require cell‐cell contact. The International Journal of Developmental Biology 49 (2–3): 309–315.

Maroto M , Bone RA and Dale JK (2012) Somitogenesis. Development (Cambridge, England) 139 (14): 2453–2456.

Monk NAM (2003) Oscillatory expression of Hes1, p53, and NF‐kappaB driven by transcriptional time delays. Current Biology: CB 13 (16): 1409–1413.

Morimoto M et al. (2005) The Mesp2 transcription factor establishes segmental borders by suppressing Notch activity. Nature 435 (7040): 354–359.

Oginuma M et al. (2010) The oscillation of Notch activation, but not its boundary, is required for somite border formation and rostral‐caudal patterning within a somite. Development (Cambridge, England) 137 (9): 1515–1522.

Okubo Y et al. (2012) Lfng regulates the synchronized oscillation of the mouse segmentation clock via trans‐repression of Notch signalling. Nature Communications 3: 1141.

Oyama T et al. (2011) Mastermind‐like 1 (MamL1) and mastermind‐like 3 (MamL3) are essential for Notch signaling in vivo. Development (Cambridge, England) 138 (23): 5235–5246.

Palmeirim I et al. (1997) Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Cell 91 (5): 639–648.

Saga Y (2012a) The mechanism of somite formation in mice. Current Opinion in Genetics & Development 22 (4): 331–338.

Schröter C et al. (2012) Topology and dynamics of the Zebrafish segmentation clock core circuitK. G. Storey, ed.. PLoS Biology 10 (7): e1001364.

Serth K et al. (2003) Transcriptional oscillation of lunatic fringe is essential for somitogenesis. Genes & Development 17 (7): 912–925.

Soroldoni D et al. (2014) Genetic oscillations. A Doppler effect in embryonic pattern formation. Science (New York, N.Y.) 345 (6193): 222–225.

Soza‐Ried C et al. (2014) Pulses of Notch activation synchronise oscillating somite cells and entrain the zebrafish segmentation clock. Development (Cambridge, England) 141 (8): 1780–1788.

Sparrow DB et al. (2013) Autosomal dominant spondylocostal dysostosis is caused by mutation in TBX6. Human Molecular Genetics 22 (8): 1625–1631.

Sparrow DB et al. (2006) Mutation of the LUNATIC FRINGE gene in humans causes spondylocostal dysostosis with a severe vertebral phenotype. American Journal of Human Genetics 78 (1): 28–37.

Sparrow DB et al. (2010) Two novel missense mutations in HAIRY‐AND‐ENHANCER‐OF‐SPLIT‐7 in a family with spondylocostal dysostosis. European Journal of Human Genetics: EJHG 18 (6): 674–679.

Takashima Y et al. (2011) Intronic delay is essential for oscillatory expression in the segmentation clock. Proceedings of the National Academy of Sciences of the United States of America 108 (8): 3300–3305.

Tiedemann HB et al. (2014) Fast synchronization of ultradian oscillators controlled by delta‐notch signaling with cis‐inhibitionD. Thieffry, ed.. PLoS Computational Biology 10 (10): e1003843.

Trofka A et al. (2012) The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub. Development (Cambridge, England) 139 (5): 940–947.

Turnpenny PD et al. (2007) Abnormal vertebral segmentation and the notch signaling pathway in man. Developmental Dynamics: An Official Publication of the American Association of Anatomists 236 (6): 1456–1474.

Webb AB et al. (2014) Generation of dispersed presomitic mesoderm cell cultures for imaging of the zebrafish segmentation clock in single cells. Journal of Visualized Experiments: JoVE 89: e50307–e50307.

Whittock NV et al. (2004) Mutated MESP2 causes spondylocostal dysostosis in humans. American Journal of Human Genetics 74 (6): 1249–1254.

Yusuf F and Brand‐Saberi B (2006) The eventful somite: patterning, fate determination and cell division in the somite. Anatomy and Embryology, 211 Suppl 1 (S1): 21–30.

Zhang Z et al. (2011) The microRNA‐processing enzyme Dicer is dispensable for somite segmentation but essential for limb bud positioning. Developmental Biology 351 (2): 254–265.

Further Reading

Graham A et al. (2014) What can vertebrates tell us about segmentation? EvoDevo 5 (1): 24.

Hubaud A and Pourquié O (2014) Signalling dynamics in vertebrate segmentation. Nature Reviews. Molecular Cell Biology 15 (11): 709–721.

Iimura T , Denans N and Pourquié O (2009) Establishment of Hox vertebral identities in the embryonic spine precursors. Current Topics in Developmental Biology 88: 201–234.

Richmond DL and Oates AC (2012) The segmentation clock: inherited trait or universal design principle? Current Opinion in Genetics & Development 22 (6): 600–606.

Saga Y (2012b) The mechanism of somite formation in mice. Current Opinion in Genetics & Development 22 (4): 331–338.

Wahi K , Bochter MS and Cole SE (2014) The many roles of Notch signaling during vertebrate somitogenesis. Seminars in Cell & Developmental Biology. DOI: 10.1016/j.semcdb.2014.11.010.

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Bailey, Charlotte, and Dale, Kim(Jun 2015) Somitogenesis in Vertebrate Development. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0003820.pub2]