University of Cambridge
TET1 AND TRANSCRIPTION FACTOR REGULATION OF LINEAGE SPECIFICATION DURING MOUSE GASTRULATION AND EARLY ORGANOGENESIS
Abstract
dc:description.abstractGastrulation and early organogenesis are overlapping events between Embryonic day (E) 6.25 and E9.5 in mouse that involve the specification of pluripotent cells into the lineage- and tissue-specific precursors of the adult organism. The dozens of cell types that arise during this period are defined by distinct transcriptional programs that depend on specific remodelling of the epigenome and Transcription Factor (TF) networks. In this thesis, I focus on the cell type-specific TFs and Ten-eleven Translocation methylcytosine dioxygenase 1 (TET1), an epigenome modifier, which regulate cell fate during gastrulation and early organogenesis in mouse. Following unbiased epigenetic and proteomic screens for TF regulators and chromatin-bound TET1 proximal (“proxisome”) proteins, I use experimental perturbations to determine novel lineage-driving TFs and TET1 epigenetic mechanisms that drive this period of development. In Chapter 1, I review recent findings in the regulation of transcriptional cell identity by DNA-binding proteins during gastrulation, with a focus on TFs and TET1. In Chapter 2, I describe the methods that I have employed to address my research questions. In Chapter 3, I explore the function of proteins that form chromatin complexes with TET1 during the TET1-regulated pluripotent-to-early neuroectoderm transition. I identify novel direct, functional interactions between TET1 and early neuroectoderm- enriched TET1 proxisome proteins macroH2A.2 and H2A.X. In Chapter 4, I integrate novel TET1 ChIP-seq and RNA-seq data with published epigenomic datasets to develop models of TET1 regulation with macroH2A.2 at bivalent genes in neuroectoderm differentiation and H2A.X at active genes in ESCs. In Chapter 5, I utilise a pooled CRISPR activation (CRISPRa) spontaneous differentiation experiment with single cell transcriptome readout to test 146 TFs with putative cell type-specific activities, based on analysis of a paired single cell transcriptome and accessibility atlas from mouse E7.5–E8.75. The experiment identifies 72 master TFs that individually bias differentiation towards or away from a specific atlas cell type. I conclude with a discussion of future analysis and experimental plans. Chapter 6 summarises my thesis work, its significance, and proposed future directions. This thesis provides novel insight into the regulation of cell identity by epigenome modifiers and TFs. In doing so, this work makes substantial contributions to the fields of bivalent chromatin biology and cell programming by TFs.
Degree
thesis:*- Name dc:type.qualificationname
- Doctor of Philosophy (PhD)
- Level dc:type.qualificationlevel
- Doctoral
- Grantor dc:publisher.institution
- University of Cambridge
- Year dc:date.issued
- 2025
Author and committee
dc:creator, dc:contributor.*- Author dc:creator
-
- Terry, Brendan
- Advisor dc:contributor.advisor
-
- Reik, Wolf
Subjects
dc:subject × 7Rights
dc:rightsIdentifiers
dc:identifier.*- DOI dc:identifier.doi
- https://doi.org/10.17863/CAM.121680
- OAI identifier oai:identifier
- oai:www.repository.cam.ac.uk:1810/389946