The development of ALICE-tRNA-sequencing and its use in exploring the role of tRNAs in translational control

Mohamed, Bashir Abdirahman (2022) The development of ALICE-tRNA-sequencing and its use in exploring the role of tRNAs in translational control. PhD thesis, University of Glasgow.

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Abstract

Sustaining proliferative signalling and loss of translational control is arguably the most fundamental trait of cancer cells, enabling tumour growth and metastatic dissemination. Transfer RNAs (tRNAs) have long been considered abundant “housekeeping” RNAs, functioning to decipher the universal genetic code. However, exhaustive analyses have implicated tRNA participation in a host of regulatory networks including the cellular stress response and protein synthesis. Recent findings suggest that the expression of tRNAs for synonymous codon usage is dependent on the differentiation/proliferation status of the cell and are coordinated with changes in translation. Although the molecular mechanisms that govern these changes are yet to be elucidated, cellular tRNA composition potentially introduces an additional layer of translational control. tRNAs are the most post-transcriptionally modified RNA species, with well over 50 unique modifications identified in eukaryotes. Consequently, isoacceptor identification and the measuring of the tRNA pool using next generation sequencing has long been an area of interest, with many attempts being made in literature. Using the Escherichia coli dealkylating enzyme AlkB and the novel tRNA high throughput sequencing methodology ALICE-tRNA-seq, we have developed a methodology that can accurately measure relative tRNA pools in vitro and in vivo. We show how other published tRNA sequencing protocols show bias towards tRNA sub populations, with our method showing a more realistic distribution across all tRNAs. We also show relative distribution changes in cellular and genetically modified mouse models of cancer, opening up a high resolution approach to establish the role of tRNAs in translational control and cell fate decisions.

Item Type: Thesis (PhD)
Qualification Level: Doctoral
Subjects: Q Science > QR Microbiology
Colleges/Schools: College of Medical Veterinary and Life Sciences > Institute of Cancer Sciences > Beatson Institute of Cancer Research
Supervisor's Name: Bushell, Professor Martin and Norman, Professor Jim
Date of Award: 2022
Depositing User: Theses Team
Unique ID: glathesis:2022-82830
Copyright: Copyright of this thesis is held by the author.
Date Deposited: 26 Apr 2022 11:28
Last Modified: 26 Apr 2022 11:30
Thesis DOI: 10.5525/gla.thesis.82830
URI: http://theses.gla.ac.uk/id/eprint/82830

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