ParaHox genes in chordate evolution and development

The ParaHox cluster comprises three genes, Gsx, Xlox/Pdx, and Cdx, which are crucial developmental regulators involved in anterior-posterior patterning of the gut and central nervous system. ParaHox genes are evolutionarily related to Hox genes and exhibit similar genomic organisation and regulatory features, including clustering and collinearity, whereby gene order correlates with spatial and/or temporal expression. Understanding how ParaHox genes are regulated, and how this regulation has evolved across chordates, offers insights into gene cluster evolution and embryonic development. Moreover, misregulation of ParaHox genes is linked to diseases such as type II diabetes and colon cancer, highlighting their biomedical relevance. This thesis investigates the regulatory architecture, evolutionary history, and functional roles of ParaHox genes in three representative chordates: Branchiostoma floridae, Ciona intestinalis, and Gallus gallus. This thesis builds on existing research by providing a broader and more detailed analysis of regulatory inputs within the ParaHox cluster, especially in amphioxus, and identifies conserved regulatory regions across other chordates. For instance, I demonstrate a cross-regulatory loop between Cdx and Xlox, suggesting an ancestral deuterostome mechanism. In addition, I show that topologically-associated domain (TAD) boundaries are conserved around intact ParaHox clusters, mirroring those seen in the Hox clusters. Several regulatory regions in amphioxus are shown to drive tissue-specific expression in Ciona, marking them as promising candidates for further analysis. This study also identifies and characterises a novel vertebrate Cdx paralogue, Cdx4-like, in Gallus gallus, which likely originated at the base of the tetrapods and is associated with calcium secretion in the oviduct. Finally, I identify beta-galactosidase as a regional marker in the ascidian gastrointestinal tract, likely regulated by ParaHox genes and potentially conserved from the bilaterian ancestor. Collectively, these findings enhance our understanding of the conservation and diversification of ParaHox gene regulation in chordate evolution and development.