Research Interests

During my doctoral research, I have been investigating the interaction of cis-regulatory modules in the transcriptional regulation of the gene myoD1. This project is supervised by Professor Georgy Koentges and Professor Mario Nicodemi.

Cis-regulatory modules (CRMs) are the functional DNA elements that encode the spatial and temporal expression patterns of a gene. Each gene is regulated by multiple CRMs, which may be hundreds of kilobases distant from the promoter. Many vertebrate CRMs have been characterised in isolation, but how CRMs act together to regulate complex patterns of expression is unknown.

I have used a flow-cytometry based reporter assay to determine the regulatory effect of combinations of CRMs in an immunologically-defined subpopulation of transfected mouse myoblast cells. Particular CRM combinations were found to have a strong synergistic effect upon reporter expression, suggesting that the CRMs do not function independently, but instead interact to regulate gene activity. Physical interactions between these sequences were confirmed using chromosome conformation capture approaches. I have used a phylogenetically-based sequence comparison method to identify conserved transcription factor binding sites in each CRM, which are likely to represent functionally important CRM components. The most promising functional candidates were characterised further using chromatin immunoprecipitation and site-directed mutagenesis. This has allowed us to identify key regulatory features within the CRM sequences and work towards a model of the myoD1 regulatory mechanism.