Supervisors: Prof. Stefan Hoppler, Dr David E.K. Ferrier
Project Description:
Summary:
This project investigates the evolution and function of Tcf genes in animal development by comparing genomes, embryonic expression and molecular functions in an interdisciplinary collaboration between biomedical and evolutionary developmental biology researchers at the Universities of Aberdeen and St Andrews.
Background:
Wnt signalling is a conserved key mechanism regulating embryogenesis, regeneration and cancer. Tcf (T-cell specific, HMG-box) is the transcription factor operating downstream of Wnt signalling. Invertebrates generally only have a single TCF gene; in contrast, humans and other vertebrates have several Tcf genes, potentially mediating more diverse functions of Wnt signalling in these embryos and during cancer progression (recently reviewed by Hoppler and Waterman, 2014). There is a gap in understanding how this diversity in vertebrate Tcf factors emerges and how it contributes to the complex functions of Wnt signalling in humans and other vertebrates. By following Dobzhansky’s famous advice: “Nothing in biology makes sense except in the light of evolution”, we aim to investigate the structural and functional evolution of Tcf genes to gain insight into Wnt signalling in biomedically relevant processes.
Aims and work programme:
Comparative genomics of Tcf
How do Tcf genes contribute to evolutionary novelty and divergence in vertebrates? A precise bioinformatic analysis of Tcf gene evolution across major vertebrate groups is essential to facilitate robust comparisons using extensive genome sequence data now available from a range of relevant species. As an out-group for these comparisons we will include closely related invertebrates, in particular the chordates amphioxus and tunicates (Garstang et al., 2016). A focus will be emergence of vertebrate-specific and functionally important protein domains, and evolutionary loss of features in certain groups. Our working hypothesis predicts that a single invertebrate Tcf gene was multiplied during two rounds of whole-genome duplication into generally four vertebrate paralogues. This analysis will provide insight into gene-specific functions of vertebrate Tcf genes and routes through which gene duplications contribute to new (neofunctionalisation) and more specific functions (subfunctionalisation).
Comparative analysis of Tcf expression
Alternative splicing produces a variety of transcripts from vertebrate Tcf genes, further increasing the variety of proteins produced. We will use PCR-based molecular methods to analyse alternative Tcf transcripts in suitable vertebrate and invertebrate species. Our findings will reveal vertebrate-specific mechanisms for modulating Wnt signalling through expression of transcripts encoding different functional domains and the extent alternative transcript expression contributes to neofunctionalisation and subfunctionalisation.
Experimental analysis of Tcf protein function
Are functions of different Tcf proteins quantitatively different (mediating stronger or weaker activation or inhibition of the same Wnt target genes) or qualitatively different (regulating different Wnt target genes)? We will test the molecular function of Tcf proteins from close invertebrate sister groups of vertebrates, from basal vertebrates, and of proteins derived from alternative transcripts. This will reveal evolutionary conserved molecular functions and identify new and more specialised functions encoded by different vertebrate genes and alternative transcripts.
Student training
Advanced bioinformatics, molecular biology and embryology techniques, including microinjection and cell culture, alongside developing fundamental concepts of molecular, developmental and evolutionary biology.
References:
Garstang, M. G., Osborne, P. W. and Ferrier, D. E. K. (2016). TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates. BMC Evol Biol 16, 57.
Hoppler, S. and Waterman, M. L. (2014). Evolutionary Diversification of vertebrate TCF/LEF structure, function, and regulation. (ed. S. Hoppler & R. T. Moon): John Wiley & Sons, Ltd.
Liu, F., Van Den Broek, O., Destrée, O. and Hoppler, S. (2005). Distinct roles for Xenopus Tcf/Lef genes in mediating specific responses to Wnt/beta-catenin signalling in mesoderm development. Development 132, 5375-5385.
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