Biologists at the California Institute of Technology (Caltech) have studied how gene networks control development in sea-urchin embryos for the last decade. Now, for the first time, they have built a predictive computation model of one of these networks.
The model encompasses the gene regulatory network that controls the first 30 hours of the development of endomesoderm cells (cells which eventually form the embryo’s gut, skeleton, muscles and immune system).
“We have never had the opportunity to explore the significance of these networks before,” said Eric Davidson, Professor of cell biology at Caltech. “The results are amazing to us.”
The model, which consists of about 50 regulatory genes, calculates how networks control the fates of different cells in the early stages of sea urchin development. The findings are published in Proceedings of the National Academy of Sciences.
The researchers created the model by distilling everything they knew about the network into a series of logical commands that a computer could process.
“We translated all of our biological knowledge into very simple Boolean statements,” Isabelle Peter, a senior research fellow, explained.
This means that the researchers represented the network as a series of if-then statements to determine whether certain genes in different cells are on or off. The model computes the results of each sequence hour by hour to determine when and where in the embryo each gene is on or off.
While some details about the network still remain to be uncovered, the model mirrors a real embryo so well that this suggests that the researchers have identified almost all of the genes necessary to control these developmental processes.
The next steps for the researchers are to model the networks responsible for every part of the sea-urchin embryo, to build a model that covers a sea urchin’s entire embryonic development.