Closing the systems biology validation gap – comparative genomics and depressive disease

Correct temporal and spatial gene expression, as well as the correct levels of gene expression, are all vital to human health. There is a danger that the recent surge in predictive systems biology brought on by genome sequencing programs may lead to the development of a systems biology “validation gap”. This gap separates the vast array of predictive genomic data from its experimental verification in the lab. In order to close this validation gap our lab utilises bioinformatics methods to firstly identify genome regions that we believe are important in gene regulation and then aims to functionally characterise these regions using a series of biologically relevant assay systems. Using comparative genomics we have identified a highly evolutionarily conserved enhancer (ECR1) of the TAC1 gene (a gene that codes for the neuropeptide Substance P (SP).
SP is a neuropeptide critical in fear and anxiety. Nothing is known about what supports the expression of this peptide in the fear centres of the brain. As a result we have created a transgenic mouse that expresses LacZ in the amygdala driven by the TAC1 enhancer ECR1. Within ECR1 we have identified a putative binding site for the glucocorticoid receptor (GR); a transcription factor involved in stress responses and also inflammatory pain. We therefore postulated that there might be a functional link between GR activity and TAC1 gene expression mediated through the ECR1 enhancer. Using a unique combination of bioinformatics, transgenic animals, organotypic brain slice culture and ChIP assay we have established a direct interaction of GR activity with the ECR1 enhancer.
The linking of GR activity to the amygdala-specific activity of the ECR1 enhancer is the first direct evidence of a mechanistic link between physiological stress and the amygdala specific expression of the TAC1 gene. This demonstrates the power of utilising systems biology approaches to understanding causes of anxiety and stress related disorders and provides novel avenues for treatment.