Somitogenesis clock-wave initiation requires differential decay and multiple binding sites for clock protein

PLoS Comput Biol. 2010 Apr 1;6(4):e1000728. doi: 10.1371/journal.pcbi.1000728.


Somitogenesis is a process common to all vertebrate embryos in which repeated blocks of cells arise from the presomitic mesoderm (PSM) to lay a foundational pattern for trunk and tail development. Somites form in the wake of passing waves of periodic gene expression that originate in the tailbud and sweep posteriorly across the PSM. Previous work has suggested that the waves result from a spatiotemporally graded control protein that affects the oscillation rate of clock-gene expression. With a minimally constructed mathematical model, we study the contribution of two control mechanisms to the initial formation of this gene-expression wave. We test four biologically motivated model scenarios with either one or two clock protein transcription binding sites, and with or without differential decay rates for clock protein monomers and dimers. We examine the sensitivity of wave formation with respect to multiple model parameters and robustness to heterogeneity in cell population. We find that only a model with both multiple binding sites and differential decay rates is able to reproduce experimentally observed waveforms. Our results show that the experimentally observed characteristics of somitogenesis wave initiation constrain the underlying genetic control mechanisms.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Basic Helix-Loop-Helix Transcription Factors / genetics
  • Basic Helix-Loop-Helix Transcription Factors / metabolism
  • Binding Sites
  • CLOCK Proteins / chemistry
  • CLOCK Proteins / genetics
  • CLOCK Proteins / metabolism*
  • DNA-Binding Proteins
  • Embryonic Development / physiology*
  • Gene Expression Regulation, Developmental / physiology*
  • Gene Knockdown Techniques
  • Models, Biological
  • Protein Binding
  • Reproducibility of Results
  • Somites / metabolism*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Zebrafish
  • Zebrafish Proteins / genetics
  • Zebrafish Proteins / metabolism


  • Basic Helix-Loop-Helix Transcription Factors
  • DNA-Binding Proteins
  • HER7 protein, zebrafish
  • Transcription Factors
  • Zebrafish Proteins
  • her1 protein, zebrafish
  • CLOCK Proteins