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Control of segment number in vertebrate embryos


The vertebrate body axis is subdivided into repeated segments, best exemplified by the vertebrae that derive from embryonic somites. The number of somites is precisely defined for any given species but varies widely from one species to another. To determine the mechanism controlling somite number, we have compared somitogenesis in zebrafish, chicken, mouse and corn snake embryos. Here we present evidence that in all of these species a similar ‘clock-and-wavefront’1,2,3 mechanism operates to control somitogenesis; in all of them, somitogenesis is brought to an end through a process in which the presomitic mesoderm, having first increased in size, gradually shrinks until it is exhausted, terminating somite formation. In snake embryos, however, the segmentation clock rate is much faster relative to developmental rate than in other amniotes, leading to a greatly increased number of smaller-sized somites.

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Figure 1: Vertebral formula and somitogenesis in the corn snake.
Figure 2: The corn snake determination front and segmentation clock.
Figure 3: Dynamics of the PSM size in zebrafish, corn snake, chicken and mouse.
Figure 4: Comparison of somitogenesis parameters.

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Data deposits

Sequences of genes described in this paper have been deposited into GenBank under accession numbers EU196456, EU196465, EU232010, EU196457, EU196458, EU196459, EU196460, EU196466, EU196461, EU196464, EU196462 and EU196463.


  1. Cooke, J. & Zeeman, E. C. A clock and wavefront model for control of the number of repeated structures during animal morphogenesis. J. Theor. Biol. 58, 455–476 (1976)

    ADS  CAS  Article  Google Scholar 

  2. Palmeirim, I., Henrique, D., Ish-Horowicz, D. & Pourquié, O. Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Cell 91, 639–648 (1997)

    CAS  Article  Google Scholar 

  3. Dequeant, M. L. & Pourquié, O. Segmental patterning of the vertebrate embryonic axis. Nature Rev . Genet. 9, 370–382 (2008)

    CAS  Google Scholar 

  4. Dequeant, M. L. et al. A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science 314, 1595–1598 (2006)

    ADS  CAS  Article  Google Scholar 

  5. Dubrulle, J., McGrew, M. J. & Pourquie, O. FGF signaling controls somite boundary position and regulates segmentation clock control of spatiotemporal Hox gene activation. Cell 106, 219–232 (2001)

    CAS  Article  Google Scholar 

  6. Sawada, A. et al. Fgf/MAPK signalling is a crucial positional cue in somite boundary formation. Development 128, 4873–4880 (2001)

    CAS  Article  Google Scholar 

  7. Aulehla, A. et al. Wnt3a plays a major role in the segmentation clock controlling somitogenesis. Dev. Cell 4, 395–406 (2003)

    CAS  Article  Google Scholar 

  8. Aulehla, A. et al. A β-catenin gradient links the clock and wavefront systems in mouse embryo segmentation. Nature Cell Biol. 10, 186–193 (2008)

    CAS  Article  Google Scholar 

  9. Richardson, M. K., Allen, S. P., Wright, G. M., Raynaud, A. & Hanken, J. Somite number and vertebrate evolution. Development 125, 151–160 (1998)

    CAS  Article  Google Scholar 

  10. Delfini, M. C., Dubrulle, J., Malapert, P., Chal, J. & Pourquie, O. Control of the segmentation process by graded MAPK/ERK activation in the chick embryo. Proc. Natl Acad. Sci. USA 102, 11343–11348 (2005)

    ADS  CAS  Article  Google Scholar 

  11. Wittler, L. et al. Expression of Msgn1 in the presomitic mesoderm is controlled by synergism of WNT signalling and Tbx6 . EMBO Rep. 8, 784–789 (2007)

    CAS  Article  Google Scholar 

  12. Nakajima, Y., Morimoto, M., Takahashi, Y., Koseki, H. & Saga, Y. Identification of Epha4 enhancer required for segmental expression and the regulation by Mesp2. Development 133, 2517–2525 (2006)

    CAS  Article  Google Scholar 

  13. Niederreither, K., Subbarayan, V., Dolle, P. & Chambon, P. Embryonic retinoic acid synthesis is essential for early mouse post-implantation development. Nature Genet. 21, 444–448 (1999)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  15. Burgess, R., Cserjesi, P., Ligon, K. L. & Olson, E. N. Paraxis: a basic helix–loop–helix protein expressed in paraxial mesoderm and developing somites. Dev. Biol. 168, 296–306 (1995)

    CAS  Article  Google Scholar 

  16. Mansouri, A. et al. Paired-related murine homeobox gene expressed in the developing sclerotome, kidney, and nervous system. Dev. Dyn. 210, 53–65 (1997)

    CAS  Article  Google Scholar 

  17. Yoon, J. K. & Wold, B. The bHLH regulator pMesogenin1 is required for maturation and segmentation of paraxial mesoderm. Genes Dev. 14, 3204–3214 (2000)

    CAS  Article  Google Scholar 

  18. Sassoon, D. et al. Expression of two myogenic regulatory factors myogenin and MyoD1 during mouse embryogenesis. Nature 341, 303–307 (1989)

    ADS  CAS  Article  Google Scholar 

  19. Pownall, M. E. & Emerson, C. P. J. Sequential activation of three myogenic regulatory genes during somite morphogenesis in quail embryos. Dev. Biol. 151, 67–79 (1992)

    CAS  Article  Google Scholar 

  20. Yoon, J. K., Moon, R. T. & Wold, B. The bHLH class protein pMesogenin1 can specify paraxial mesoderm phenotypes. Dev. Biol. 222, 376–391 (2000)

    CAS  Article  Google Scholar 

  21. McGrew, M. J., Dale, J. K., Fraboulet, S. & Pourquie, O. The lunatic Fringe gene is a target of the molecular clock linked to somite segmentation in avian embryos. Curr. Biol. 8, 979–982 (1998)

    CAS  Article  Google Scholar 

  22. Forsberg, H., Crozet, F. & Brown, N. A. Waves of mouse Lunatic fringe expression, in four-hour cycles at two-hour intervals, precede somite boundary formation. Curr. Biol. 8, 1027–1030 (1998)

    CAS  Article  Google Scholar 

  23. Zug, G. R., Vitt, L. J. & Caldwell, J. P. Herpetology: an Introductory Biology of Amphibians and Reptiles 2nd edn (Academic, San Diego, 2001)

    Google Scholar 

  24. Tam, P. P. The control of somitogenesis in mouse embryos. J. Embryol. Exp. Morphol. 65 (Suppl). 103–128 (1981)

    PubMed  Google Scholar 

  25. Primmett, D. R., Norris, W. E., Carlson, G. J., Keynes, R. J. & Stern, C. D. Periodic segmental anomalies induced by heat shock in the chicken embryo are associated with the cell cycle. Development 105, 119–130 (1989)

    CAS  Article  Google Scholar 

  26. Giudicelli, F., Ozbudak, E. M., Wright, G. J. & Lewis, J. Setting the tempo in development: an investigation of the zebrafish somite clock mechanism. PLoS Biol. 5, e150 (2007)

    Article  Google Scholar 

  27. Cambray, N. & Wilson, V. Two distinct sources for a population of maturing axial progenitors. Development 134, 2829–2840 (2007)

    CAS  Article  Google Scholar 

  28. Sanders, E. J., Khare, M. K., Ooi, V. C. & Bellairs, R. An experimental and morphological analysis of the tail bud mesenchyme of the chicken embryo. Anat. Embryol. (Berl.) 174, 179–185 (1986)

    CAS  Article  Google Scholar 

  29. Shum, A. S. et al. Retinoic acid induces down-regulation of Wnt-3a, apoptosis and diversion of tail bud cells to a neural fate in the mouse embryo. Mech. Dev. 84, 17–30 (1999)

    CAS  Article  Google Scholar 

  30. Henrique, D. et al. Expression of a Delta homologue in prospective neurons in the chicken. Nature 375, 787–790 (1995)

    ADS  CAS  Article  Google Scholar 

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The authors thank M. Gibson, B. Rubinstein, P. Francois and members of the Pourquié laboratory for critical reading and discussions, M. Wahl for the mouse LFNG pictures, members of the Reptile and Aquatics Department, J. Chatfield for editorial assistance, and S. Esteban for artwork. Research was supported by Stowers Institute for Medical Research, and in part by a Defense Advanced Research Projects Agency (DARPA) grant (O.P.). J.L. is supported by Cancer Research UK. Zebrafish were obtained from the Zebrafish International Resource Center (ZIRC) at the University of Oregon, which is supported by a grant from the NIH-NCRR. O.P. is a Howard Hughes Medical Institute Investigator.

Author Contributions C.G. and O.P. designed the experiments, C.G. cloned the snake genes and performed the mouse, chicken and snake in situ hybridizations, E.M.O. performed the fish in situs, C.G. and E.M.O. performed the measurements and analysed the data with O.P. D.B. established the corn snake and zebrafish colony and produced the embryos. C.G. and J.W. performed the cell cycle analysis. J.L. performed the mathematical modelling. C.G., E.M.O., J.L. and O.P. wrote the manuscript. All authors discussed the results and commented on the manuscript.

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Correspondence to Olivier Pourquié.

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The file contains Supplementary Methods with additional references, Supplementary Figures 1-5 with Legends, Supplementary Tables 1-4 and Supplementary Boxes 1-2. (PDF 4543 kb)

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Gomez, C., Özbudak, E., Wunderlich, J. et al. Control of segment number in vertebrate embryos. Nature 454, 335–339 (2008).

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