Universität zu Köln

Müller, Jason Marcel (2023). Resolving the mRNA Life Cycle across Cell Compartments. PhD thesis, Universität zu Köln.

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Abstract

In a eukaryotic cell, the life cycle of an mRNA consists of several processing steps, including its synthesis, export from the nucleus into the cytosol, and, after fulfilling its function as a protein template, cytosolic degradation. Eventually, the transcript can also be degraded in the nucleus upon aberrant processing. Yet, the dynamics of these processes that determine how mRNA flows through the cell are still not fully understood. Understanding these dynamics is crucial as impairments in mRNA metabolism have been associated with severe human diseases. Recent advances in biotechnology allow for the investigation of eukaryotic mRNA metabolism by combining metabolic labeling sequencing techniques with subcellular fractionation protocols. In such experiments, newly synthesized mRNA is labeled with nucleoside analogs that allow for differentiation of pre-existing transcripts. However, the analysis of this data provides many computational challenges. In this dissertation, I develop a model to quantify essential parameters of eukaryotic mRNA metabolism, from which nuclear and cytosolic RNA half-lives can be derived. The model uses metabolic labeling sequencing data from HeLa-S3 cells that were separated into nuclear and cytosolic compartments by subcellular fractionation prior to sequencing. The presented method is demonstrated to overcome critical biases of metabolic labeling sequencing data. At the same time, it outperforms the corresponding methodology of the widely used tool GRAND-SLAM for analyzing such data. The model reveals that nuclear export is slow, while cytosolic degradation is fast. Consequently, an average mRNA spends most of its life in the nucleus, not the cytosol. I show that mRNA metabolism is consistent along the cell cycle, and its quantities can be used to pinpoint potential regulators of metabolic subprocesses such as nuclear export. In summary, the presented model resolves the life cycle of an eukaryotic mRNA across cell compartments with high accuracy and, therefore, will be a valuable tool for RNA research.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Müller, Jason Marcel jason.mueller@uni-koeln.de UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-725071
Date:	2023
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Medicine > Medizinische Statistik und Bioinformatik > Institut für Medizinische Statistik und Bioinformatik – IMSB
Subjects:	Natural sciences and mathematics Life sciences
Uncontrolled Keywords:	Keywords Language Computational Biology UNSPECIFIED RNA Metabolism UNSPECIFIED RNA Labeling UNSPECIFIED
Date of oral exam:	20 March 2024
Referee:	Name Academic Title Tresch, Achim Prof. Dr Beyer, Andreas Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/72507