My Project

My main area of research is the Arabidopsis circadian clock. I'm interested in targets of the core clock genes LHY and CCA1, which are currently thought to operate in a negative feedback loop with TOC1. Both LHY and CCA1 are transcription factors in the MYB family, and are known to bind to a sequence called the Evening Element (AAATATCT). Many genes containing the Evening Element motif show different expression profiles, and the aim of my project is to identify what it is that modulates LHY/CCA1 binding, and whether the protein has an activatory or inhibitory effect on transcription of target genes. My bioinformatic work is supervised by Sascha Ott, in Warwick Systems Biology Centre, and experimental work by Isabelle Carré in the Department of Biological Sciences.

I have developed a comparative genomics approach to elucidate potential binding sites in the promoters of clock genes, searching for their orthologs in other species and then using alignment-based methods to uncover regions conserved in all species. More details can be found in our paper "Evolutionary Analysis of Regulatory Sequences (EARS) in Plants". The next step of the analysis is to search to see if any of these motifs are enriched in genes expressed at certain times of the day.

The experimental complement to the project is to test whether these newly identified elements are functional binding sites. Promoter fusions to the firefly luciferase gene have been produced with mutations in these binding sites, and then transformed into plants. This allows the use of luciferase imaging to follow expression in real time, and look for alterations to the normal circadian pattern.