Universität zu Köln

Titz-Teixeira, Fabian ORCID: 0000-0002-7007-9039 (2024). Gene Regulatory Dependencies in Mouse Embryonic Stem Cells. PhD thesis, Universität zu Köln.

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Abstract

The pluripotency of embryonic stem cells (ESCs) is defined by their capacity for self-renewal and differentiation into any cell type of an organism. These two characteristics, combined with the ability to induce pluripotency, harbor great potential to apply pluripotent cells in different fields of research and medicine. In contrast to the well-studied state of pluripotency, the cellular networks that disrupt the self-renewal program and promote the exit from pluripotency are poorly characterized. This thesis aims to investigate the networks that promote differentiation and break the self-renewal circuit, thus leading to cells transitioning from naïve to formative pluripotency. We conducted a comprehensive analysis of multiple datasets reflecting the naïve to formative transition to elucidate the mechanisms that drive differentiation. A dense 32-hour wildtype (WT) differentiation time course was utilized to quantify the differentiation delay of 73 mouse knockout (KO) cell lines exhibiting altered differentiation. The comparison of the delays of the naïve and formative networks suggested a decoupling between both networks in their exit from naïve pluripotency. Furthermore, we investigated gene regulatory dependencies between genes in the naïve to formative transition. For this purpose, we developed two methods to infer gene regulatory dependencies from the KO data and an independent single-cell (sc) WT differentiation time course. The resulting dependencies of both approaches showed high concordance and revealed that the transcriptional adaptation of the formative network is independent of the naïve network. Additionally, we observed that parts of the formative network had already adapted to differentiation despite inhibiting fibroblast growth factor/extracellular signal-regulated kinase (FGF/ERK) signaling, indicating FGF/ERK independent regulation of the formative network. Moreover, we provided potential upstream regulators of the formative network based on integrating publicly available ATAC-seq data and a database of transcription factor (TF) motifs. In summary, we show that the transcriptional adaptation of the formative network surprisingly is independent of the naïve network. Thus, whereas the naïve pluripotency network is essential for maintaining pluripotency, genes required to establish subsequent cellular states are under distinct regulatory input.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Titz-Teixeira, Fabian UNSPECIFIED orcid.org/0000-0002-7007-9039 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-732905
Date:	2024
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	CECAD - Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases
Subjects:	Data processing Computer science Life sciences
Uncontrolled Keywords:	Keywords Language embryonic stem cells UNSPECIFIED pluripotency UNSPECIFIED
Date of oral exam:	29 May 2024
Referee:	Name Academic Title Beyer, Andreas Prof. Dr. Tresch, Achim Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/73290