Control of the ParaHox genes in chordate evolution and development

Supervisors: David E.K. Ferrier, Kate G. Storey

Project Description:
This project will use a comparative approach to dissect the regulatory mechanisms of the chordate ParaHox genes (Gsx, Xlox/Pdx1 and Cdx), analysing regulatory elements of these genes in both the invertebrate sea squirt Ciona intestinalis and the vertebrate Gallus gallus (chicken).

ParaHox genes are the evolutionary sisters to the Hox genes, and like their sisters are important components of axial patterning, mainly in the central nervous system and gut. They also tend to have a clustered organisation in the genome that is likely linked to how the genes are regulated. Mis-regulation of ParaHox genes can cause diseases such as diabetes and colon cancer.

A major open question is whether an ancestral mechanism for Hox/ParaHox regulation can be deduced, which would provide both a fundamental insight into animal development and reveal the starting point from which the current regulatory diversity evolved. Understanding ParaHox regulation is a key route to achieving this goal. Since the split into Hox and ParaHox clusters occurred early in animal evolution [1], comparisons of ParaHox and Hox regulation can potentially reveal what is conserved between these sister clusters and hence what mechanisms were involved in control of these genes in the earliest animals, with these fundamental mechanisms then underpinning all subsequent evolution.

In this project, we will integrate data from both invertebrate and vertebrate systems, capitalizing on the power of the comparative approach to deduce underlying fundamental aspects of body axis patterning by regulation of the ParaHox genes. The main invertebrate model will be the sea squirt Ciona intestinalis, in which large numbers of embryos can be rapidly transformed by electroporation [2] and for which large data-sets of DNA sequence and gene expression are available. The vertebrate model will be the chicken, Gallus gallus, due to its compact, intact ParaHox cluster, well-established suitability as an embryological study system and available techniques in embryo electroporation and gene expression analyses [3].

Regulatory elements will be characterised via generation of reporter genes around each of the Ciona ParaHox genes as well as from across the entire chicken ParaHox cluster. This will enable a direct comparison of an intact and a dispersed ParaHox cluster. Reporter construction will be aided by bioinformatic comparisons of these genomic loci across the invertebrate chordate and vertebrate genome sequences that are already available. Minimal regulatory elements will be isolated via deletion mapping of reporters and candidate transcription factors deduced via bioinformatic analyses, comparisons to expression databases and site-directed mutagenesis and/or in vitro binding assays. This will establish what regulatory factors are operating across the ParaHox genes, potentially throughout the chordate phylum, and will form the basis for comparisons to regulation of the Hox genes to establish whether the same fundamental regulatory mechanisms might be operating across the animals.

The student will obtain training in cutting-edge techniques in molecular biology, embryology, bioimaging and bioinformatics and be part of the enthusiastic and vibrant research communities in the Universities of St Andrews and Dundee, benefitting from the complementary strengths, strong links and close proximity of these institutions.


1) Fortunato, S.A.V., Adamski, M., Mendivil Ramos, O., Leininger, S., Liu, J., Ferrier, D.E.K. and Adamska, M. Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Nature (2014) 514, 620-623.

2) Garstang, M.G., Osborne, P.W., and Ferrier, D.E.K. TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates. BMC Evolutionary Biology (2016) 16: 57.

3) Olivera-Martinez I, Harada H, Halley PA, Storey KG. Loss of FGF-dependent mesoderm identity and rise of endogenous retinoid signalling determine cessation of body axis elongation. PLoS Biol. (2012)10(10):e1001415.