Floc'hlay2020 - SeaUrchin_model_ginsim

  public model
Model Identifier
MODEL2002190001
Short description
Multilevel logical model encompassing the Nodal and BMP pathways together with key transcription factors setting the dorsal-ventral axis in the sea urchin P. lividus embryo. This model accounts for the specification of wild-type ventral ectoderm, ciliary band and dorsal ectoderm, and further recapitulates sophisticated mutant phenotypes.
Format
SBML (L3V1)
Related Publication
  • Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo.
  • Floc'hlay S, Molina MD, Hernandez C, Haillot E, Thomas-Chollier M, Lepage T, Thieffry Denis
  • Development (Cambridge, England) , 12/ 2020 , PubMed ID: 33298464
  • Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.
  • During sea urchin development, secretion of Nodal and BMP2/4 ligands and their antagonists Lefty and Chordin from a ventral organizer region specifies the ventral and dorsal territories. This process relies on a complex interplay between the Nodal and BMP pathways through numerous regulatory circuits. To decipher the interplay between these pathways, we used a combination of treatments with recombinant Nodal and BMP2/4 proteins and a computational modelling approach. We assembled a logical model focusing on cell responses to signalling inputs along the dorsal-ventral axis, which was extended to cover ligand diffusion and enable multicellular simulations. Our model simulations accurately recapitulate gene expression in wild type embryos, accounting for the specification of ventral ectoderm, ciliary band and dorsal ectoderm. Our model simulations further recapitulate various morphant phenotypes, reveals a dominance of the BMP pathway over the Nodal pathway, and stresses the crucial impact of the rate of Smad activation in D/V patterning. These results emphasise the key role of the mutual antagonism between the Nodal and BMP2/4 pathways in driving early dorsal-ventral patterning of the sea urchin embryo.
Contributors
Denis Thieffry, Krishna Kumar Tiwari

Metadata information

hasProperty
Mathematical Modelling Ontology Logical model

Curation status
Non-curated

Modelling approach(es)

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Model files

SeaUrchin_model_ginsim.sbml Logical model of the regulatory network controlling DV Patterning in P lividus (SBML L3VI qual). 65.02 KB Preview | Download

  • Model originally submitted by : Denis Thieffry
  • Submitted: Jan 6, 2021 12:13:25 PM
  • Last Modified: Jan 6, 2021 12:13:25 PM
Revisions
  • Version: 6 public model Download this version
    • Submitted on: Jan 6, 2021 12:13:25 PM
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Edited model metadata online.
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