Dynamic Modeling of Transcriptional Gene Regulatory Networks

Diverse cellular phenotypes are determined by groups of transcription factors (TFs) and other regulators that influence each others' gene expression, forming transcriptional gene regulatory networks (GRNs). In many biological contexts, especially in development and associated diseases, the expression of the genes in GRNs is not static but evolves in time. Modeling the dynamics of GRN state is an important approach for understanding diverse cellular phenomena such as cell-fate specification, pluripotency and cell-fate reprogramming, oncogenesis, and tissue regeneration. In this protocol, we describe how to model GRNs using a data-driven dynamic modeling methodology, gene circuits. Gene circuits do not require knowledge of the GRN topology and connectivity but instead learn them from training data, making them very general and applicable to diverse biological contexts. We utilize the MATLAB-based gene circuit modeling software Fast Inference of Gene Regulation (FIGR) for training the model on quantitative gene expression data and simulating the GRN. We describe all the steps in the modeling life cycle, from formulating the model, training the model using FIGR, simulating the GRN, to analyzing and interpreting the model output. This protocol highlights these steps with the example of a dynamical model of the gap gene GRN involved in Drosophila segmentation and includes example MATLAB statements for each step.