Logical model of the regulatory network controlling dorsal-ventral axis specification in the sea urchin P. lividius
Taxon: Sea Urchin
Process: Development
Submitter: Pedro Monteiro
Supporting paper: Floc'hlay, Swann and Molina, Maria Dolores and Hernandez, Céline and Haillot, Emmanuel and Thomas-Chollier, Morgane and Lepage, Thierry and Thieffry, Denis (2020). Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo. Development. 10.1242/dev.189944
| Model file(s) | Description(s) |
|---|---|
| SeaUrchin_model_ginsim.zginml | Unicellular model in zginml format (to be used with GINsim 3.0) |
| Flochlay_SeaUrchin_DV_model.sbml | Corresponding BioModels entry (SBML qual format) |
| Flochlay_SeaUrchin_model_epilog.peps | Multicellular model in peps format (to be used with Epilog v1.1.1) |
| Flochlay_SeaUrchin_notebook.ipynb | Jupiter Notebook (to be used with the colomoto-docker image) |
Summary:
We have integrated novel experimental results with previous data about the
roles of Nodal and BMP pathways in early development of Paracentrotus lividus
in the form of a regulatory graph, which was complemented with logical rules,
thereby enabling the simulation of cell responses to varying signalling inputs
along the dorsal-ventral axis. This logical model was then extended to account
for ligand diffusion and enable multicellular simulations, which accurately
recapitulated gene expression in wild type embryos, accounting for the
specification of the three main ectodermal regions, namely ventral ectoderm,
ciliary band and dorsal ectoderm, and further recapitulated sophisticated
mutant phenotypes. Finally, using a stochastic extension of the logical
formalism, we performed more quantitative temporal simulations, which revealed
a dominance of the BMP pathway over the Nodal pathway, and pointed to the rate
of Smad activation as a key parameter for D/V patterning of the embryo.
The links below enable the download of i) the unicellular GINsim model (zginml format, to be open with GINsim 3.0), the multicellular model (peps format, to be open with Epilog v1.1.1), and ii) the jupyter notebook containing the code of all the analyses (to be used with the colomoto-docker image).