Tomlinson, Joe
(2025)
Bioinformatic investigation of downstream open reading frames and their role in post-transcriptional regulation of gene expression.
PhD thesis, University of Nottingham.
Abstract
Downstream open reading frames (dORFs) are short open reading frames in 3' untranslated regions (3’ UTRs) of messenger RNAs (mRNAs) that are proposed to regulate translation. dORF translation has been suggested to increase the translation of a transcript. Ribosomes are present in 3’ UTRs, and this can be influenced by local cellular conditions. The importance of dORFs is highlighted by many diseases, including cancer, which are linked to dysfunction of translational regulation or post-transcriptional regulators.
This project used a bioinformatic approach and publicly available datasets to investigate translational regulation, focussing on dORFs and their role in translational regulation in cancers. Paired RNA sequence (RNAseq) and ribosome profiling (RP) datasets were used to investigate translational regulation of transcripts with and without dORFs and ribosome association with 3’ UTRs and dORFs. Paired healthy and cancer datasets were compared. The abundance of potential dORFs in 3’ UTRs was investigated and comparison of dORF nucleotide, dinucleotide, and trinucleotide composition with 3’ UTRs and coding sequences (CDSs) was determined. The conservation of dORFs was explored, including comparison with flanking sequences and 3’ UTRs more generally. Further RP datasets were analysed to determine whether different cell types, cellular conditions, and disease states influenced ribosomal association with dORFs and dORF-containing 3’ UTRs.
Generally, in healthy tissue, transcripts containing dORFs reported in Wu et al. (2020b) were translationally upregulated compared to transcripts without. The activity of these dORFs reduced in tumour tissue, which is unlikely to be explained by transcript alterations, such as 3’ UTR truncation, in the tumour datasets. dORFs were found to share more similar nucleotide, dinucleotide and trinucleotide composition with the noncoding 3’ UTRs than CDSs. dORFs with ribosome association are widespread, however most dORFs had low ribosomal association and little evidence of translational regulation, in contrast to the dORFs reported in Wu et al. (2020b). dORF ribosomal association was varied and likely influenced by different cell types, disease states and local conditions. The biological importance of dORFs is emphasised by their conservation across species. dORFs are more conserved than flanking sequences and 3’ UTRs generally. Some dORFs may be translational regulators, whereas others may have activity through an encoded peptide. Further investigation is needed to understand the mechanism of action and function of dORFs, which are a novel, interesting, and important feature of mRNAs.
| Item Type: |
Thesis (University of Nottingham only)
(PhD)
|
| Supervisors: |
Spriggs, Keith
Blanchard, Adam
Piccinini, Anna |
| Keywords: |
Bioinformatics, Downstream open reading frames, dORF, Post-transcriptional, 3' UTR, Gene Regulation, translational regulation |
| Subjects: |
Q Science > QH Natural history. Biology > QH301 Biology (General)
Q Science > QH Natural history. Biology > QH426 Genetics
R Medicine > RC Internal medicine > RC 254 Neoplasms. Tumors. Oncology (including Cancer) |
| Faculties/Schools: |
UK Campuses > Faculty of Science > School of Pharmacy |
| Item ID: |
81872 |
| Depositing User: |
Tomlinson, Joe
|
| Date Deposited: |
12 Dec 2025 04:40 |
| Last Modified: |
12 Dec 2025 04:40 |
| URI: |
https://eprints.nottingham.ac.uk/id/eprint/81872 |
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