Towards a gene regulatory network for otic and epibranchial specification

Student thesis: Doctoral ThesisDoctor of Philosophy


Vertebrate sensory organs arise from the pre-placodal region (PPR) at the border of the neural plate, specified early during development. Differential activation of signalling pathways along the rostro-caudal axis patterns this territory to give rise to distinct placodes and ultimately to the olfactory epithelium, lens, inner ear and cranial ganglia. The aim of this project is to further investigate how sensory progenitor cells are restricted in fate to become specified as otic and epibranchial cells.
The otic placode is induced next to the developing hindbrain by a combination of FGF and WNT signalling, while the epibranchial placode is specified by sustained FGF signalling and BMPs. Downstream of these signals different transcription factors are activated sequentially to confer otic-epibranchial fate. However, their epistatic relationships and regulatory interactions are poorly understood. Gene regulatory networks (GRNs) are powerful tools to explain why cells behave the way they do and here I aim to uncover the network that controls otic-epibranchial specification. To this end, I have combined published data with results from new molecular screens to generate a preliminary GRN that contains around 50 otic and epibranchial specific transcription factors and their signalling inputs.
To establish the hierarchical interaction between all network components and their response to otic inducing signals I designed systematic perturbation experiments and exploited NanoString technology to quantify each component in the same tissue sample. Manipulation of signalling inputs reveals a temporal hierarchy of otic specification genes and points to a highly dynamic interaction between them. To identify new epistatic relationships among otic transcription factors, I employed loss-of-function approaches for key network components. In a complementary approach, I investigated the contribution of FGF on the otic chromatin landscape by ChIP-seq for histone modifications. Bioinformatic tools were used to interpret the data and regulatory elements for early FGF response genes were identified experimentally.
The emerging GRN will not only identify new key regulators for inner ear specification, but also the regulatory regions that integrate information to build a functional ear.
Date of Award2015
Original languageEnglish
Awarding Institution
  • King's College London
SupervisorAndrea Streit (Supervisor) & Albert Basson (Supervisor)

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