The identification of Transcription Factors' combinatorial binding in human development.

Abstract

Transcription Factors (TFs) are proteins that bind to cis-regulatory elements, like enhancers, to regulate gene expression. TFs do not bind to enhancers in isolation; they bind in combination to each other, allowing for tightly spatially and temporally controlled gene expression regulation. Thus, combinatorial binding to enhancers is essential during embryonic development to ensure controlled activation of gene networks, resulting in the correct cell types being formed at the right stage and embryonic location. TFs have a DNA binding domain, which can recognise short DNA sequences and is often conserved across members of the same TF family. This domain can be represented as a position weight matrix (PWMs). The availability of PWMs identified through experiments has advanced the bioinformatics field, allowing researchers to predict binding events using computational methods and publicly available experimental data. In this thesis, coscoTF, a bioinformatics method to predict context-specific co-occurrence of TF motifs, is presented. This method uses PWMs of context-specific TFs and high-confidence context-specific regulatory elements as input. CoscoTF is used in a case study to characterise TF combinatorial binding at human developmental tissue-specific enhancers, active during organogenesis. The results reveal enrichment of motifs belonging to ubiquitous TF family TEAD proximal to tissue-specific TF motifs across multiple tissues. We focus on the enrichment of TEAD motifs within 100nt of GATA motifs in ventricle-specific enhancer and within 100nt of CRX motifs in retinal pigmented epithelium-specific enhancers to experimentally validate coscoTF's predictions and to investigate what role TEAD TFs, particularly TEAD1, might be playing at tissue-specific enhancers. Results reveal that TEAD1 can repress tissue-specific activity at developmental enhancers, in fact, across experiments performed in this study, TEAD1 only carries out its repressive role when bound proximal to a tissue-specific TF. Overall this thesis presents a method that can successfully predict functional context-specific co-occurrence of motifs. We find that ubiquitous TFs are a central component of the tissue-specific developmental enhancer landscape. Supported by evidence presented in this thesis and the literature, we propose that TEAD1 antagonises tissue-specific activators bound at developmental tissue-specific enhancers to inhibit or slow down cell differentiation whilst promoting cell proliferation. Furthermore, given that TEAD motifs are enriched across numerous tissues, we propose that TEAD binding to developmental enhancers to repress transcriptional activator activity could contribute to TEAD's role as the effector of the hippo pathway, coordinating organ growth across the embryo.

Date of Award	31 Dec 2023
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Dave Gerrard (Supervisor), Nicoletta Bobola (Supervisor) & Neil Hanley (Supervisor)