An iterative pipeline of computational modelling and experimental design for uncovering gene regulatory networks in vertebrates

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The behaviour of biological systems is the result of multiple regulatory interactions. Gene regulatory networks (GRNs) are the representation of these complex molecular interactions. They help us to understand how relationships between molecules dictate cell behaviour and are particularly useful to understand the complex dynamical processes driving animal development. The nodes in a GRN represent genes. Links between genes determine which gene products (proteins) regulate which other genes. In this project we focus on transcriptional regulation. This control mechanism regulates which genes are transcribed and expressed in the cell (and eventually which proteins are synthesized). The gene products that regulate transcription are a class of proteins called transcription factors. Transcription factors bind the DNA of target genes and influence the rate at which the target genes are transcribed. Mathematical models can describe how the rate of target gene transcription is affected when transcription factors bind to the DNA, and are useful to understand how cellular-scale behaviours arise from molecular actions. In this project we aim to develop computational methods able to construct GRN models using experimental data that describe gene expression and experimental data that describe the location of bound transcription factor proteins in DNA. An important aspect of the project is the development of a methodology capable of iteratively improving the GRN model by designing the most informative and effective sequence of experiments to be performed. This is particularly important since the experiments to locate binding of transcription factors to DNA are time-consuming and expensive and care should be taken to choose the most useful experiment at each stage. The methodology developed will be used to construct the GRN controlling the development of the second branchial arch (IIBA) in mouse. Branchial arches are transient structures of all vertebrate embryos that will eventually contribute to the face and the neck. Development of the IIBA is controlled by Hoxa2, a member of the large family of Hox transcription factors (TF). Hox TFs regulate morphogenesis along the head-tail axis of all animals with bilateral symmetry, but their mechanism of action is mostly unknown in vertebrates. Uncovering the principles underlying the GRN responsible for IIBA development will help us to understand the function of many other systems that are controlled by Hox proteins in vertebrate embryogenesis.