Evolution of Chordate ParaHox Gene Regulation

The project will involve an investigation into the chordate ParaHox gene cluster, specifically looking at
the regulatory mechanisms operating across them. ParaHox genes are the evolutionary sister to the Hox
genes and too exhibit collinearity in expression. A particular advantage of studying the ParaHox genes
is that there are only three ParaHox genes, which provides a simpler system to investigate in comparison
to the Hox genes.
The organisms used to study these genes will be amphioxus, the tunicate ciona and the chick. Providing
the means to look at the role of the cluster both before and after the two rounds of whole genome
duplication at the base of the vertebrates. Using all three organisms also provides the opportunity to look
at both intact and dispersed clusters. Overall, comparisons between the three species will be used to
investigate the role of the Parahox genes in the evolution and diversification of the earliest animals.
The project will achieve this by identifying conservation in upstream regions of our genes of interest using
programs like VISTA and MULAN to identify conserved transcription factor binding sites within this region.
Following identification of potential transcription factors, in-situ hybridisation could be used to compare
expression across the three species. Expansion on this could be to use gene knock out using Crispr or
targeted mutanogenesis (can introduce double point mutations) compare between the different
organisms.