Gene regulatory networks during zebrafish endoderm development

Student thesis: Doctoral ThesisDoctor of Philosophy


During development, gene regulatory networks control cell fate decisions and differentiation leading to formation of the adult organism. A critical part of this process is the establishment of the three germ layers – ectoderm, mesoderm and endoderm. The endoderm, the inner germ layer, gives rise to the respiratory and gastrointestinal tracts and contributes to organs such as the pancreas, liver and lungs. The establishment of this germ layer is a process dependent on the integration of multiple transcriptional and signalling inputs, and while the formation of ectoderm and mesoderm have been studied extensively, our knowledge about the regulatory network controlling endoderm development is still limited. The aim of my PhD is to investigate the network of transcription factors that determine the specification of endodermal lineage in zebrafish and how these factors integrate and interact to bring about correct gene expression. In order to do so, I combine both experimental and computational methodologies. Firstly, I focus on the role of Sox and Mix family members and their interactions with binding partners in specifying and patterning endodermal cells during gastrulation. I use ChIP-exo, a form of chromatin immunoprecipitation combined with exonuclease digestion and high-throughput sequencing, to try and identify genomic positions bound by the different transcription factors. I then isolate endodermal cells by flow cytometry using a transgenic line carrying a fluorescent reporter gene, tg(sox17:GFP), in order to characterise the transcriptomic signature of developing endodermal cells. Finally, I combine the data generated together with existing published data sets to construct the gene regulatory network underpinning endodermal fate in zebrafish. Together, these findings extend our understanding of embryonic endodermal development, and move us one step closer to reconstructing the pattern of genetic regulation that happens during the developmental specification of endoderm. This knowledge will ultimately help us to formulate a comprehensive map detailing how a pluripotent cell in the zebrafish embryo becomes committed to an endodermal fate.
Date of Award1 Aug 2019
Original languageEnglish
Awarding Institution
  • King's College London
SupervisorFiona Wardle (Supervisor) & Anthony Graham (Supervisor)

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