A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profiles Export

@article{citeulike:353214, abstract = {Flowers are icons in developmental studies of complex structures. The vast majority of 250,000 angiosperm plant species have flowers with a conserved organ plan bearing sepals, petals, stamens, and carpels in the center. The combinatorial model for the activity of the so-called ABC homeotic floral genes has guided extensive experimental studies in Arabidopsis thaliana and many other plant species. However, a mechanistic and dynamical explanation for the ABC model and prevalence among flowering plants is lacking. Here, we put forward a simple discrete model that postulates logical rules that formally summarize published ABC and non-ABC gene interaction data for Arabidopsis floral organ cell fate determination and integrates this data into a dynamic network model. This model shows that all possible initial conditions converge to few steady gene activity states that match gene expression profiles observed experimentally in primordial floral organ cells of wild-type and mutant plants. Therefore, the network proposed here provides a dynamical explanation for the ABC model and shows that precise signaling pathways are not required to restrain cell types to those found in Arabidopsis, but these are rather determined by the overall gene network dynamics. Furthermore, we performed robustness analyses that clearly show that the cell types recovered depend on the network architecture rather than on specific values of the model's gene interaction parameters. These results support the hypothesis that such a network constitutes a developmental module, and hence provide a possible explanation for the overall conservation of the ABC model and overall floral plan among angiosperms. In addition, we have been able to predict the effects of differences in network architecture between Arabidopsis and Petunia hybrida. 10.1105/tpc.104.021725}, address = {Instituto de Ecolog\'{\i}a, Universidad Nacional Aut\'{o}noma de M\'{e}xico, Mexico, Distrito Federal 04510.}, author = {Espinosa-Soto, Carlos and Padilla-Longoria, Pablo and Alvarez-Buylla, Elena R.}, citeulike-article-id = {353214}, citeulike-linkout-0 = {http://dx.doi.org/10.1105/tpc.104.021725}, citeulike-linkout-1 = {http://www.plantcell.org/cgi/content/abstract/16/11/2923}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/15486106}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=15486106}, day = {1}, doi = {10.1105/tpc.104.021725}, issn = {1040-4651}, journal = {Plant Cell}, keywords = {arabidopsis, genetic\_regulatory\_networks, modelling}, month = {November}, number = {11}, pages = {2923--2939}, posted-at = {2007-01-25 02:21:16}, priority = {4}, title = {A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profiles}, url = {http://dx.doi.org/10.1105/tpc.104.021725}, volume = {16}, year = {2004} }

TY - JOUR ID - citeulike:353214 L3 - citeulike-article-id:353214 N2 - Flowers are icons in developmental studies of complex structures. The vast majority of 250,000 angiosperm plant species have flowers with a conserved organ plan bearing sepals, petals, stamens, and carpels in the center. The combinatorial model for the activity of the so-called ABC homeotic floral genes has guided extensive experimental studies in Arabidopsis thaliana and many other plant species. However, a mechanistic and dynamical explanation for the ABC model and prevalence among flowering plants is lacking. Here, we put forward a simple discrete model that postulates logical rules that formally summarize published ABC and non-ABC gene interaction data for Arabidopsis floral organ cell fate determination and integrates this data into a dynamic network model. This model shows that all possible initial conditions converge to few steady gene activity states that match gene expression profiles observed experimentally in primordial floral organ cells of wild-type and mutant plants. Therefore, the network proposed here provides a dynamical explanation for the ABC model and shows that precise signaling pathways are not required to restrain cell types to those found in Arabidopsis, but these are rather determined by the overall gene network dynamics. Furthermore, we performed robustness analyses that clearly show that the cell types recovered depend on the network architecture rather than on specific values of the model's gene interaction parameters. These results support the hypothesis that such a network constitutes a developmental module, and hence provide a possible explanation for the overall conservation of the ABC model and overall floral plan among angiosperms. In addition, we have been able to predict the effects of differences in network architecture between Arabidopsis and Petunia hybrida. 10.1105/tpc.104.021725 IS - 11 JF - Plant Cell SN - 1040-4651 AD - Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico, Distrito Federal 04510. EP - 2939 TI - A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profiles VL - 16 SP - 2923 KW - arabidopsis KW - genetic_regulatory_networks KW - modelling AU - Espinosa-Soto, Carlos AU - Padilla-Longoria, Pablo AU - Alvarez-Buylla, Elena PY - 2004/11/01/ UR - http://dx.doi.org/10.1105/tpc.104.021725 ER -