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Transcriptomic analysis predicts the identities and biological roles of Campylobacter jejuni small RNAs
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Li, Stephen (2022) Transcriptomic analysis predicts the identities and biological roles of Campylobacter jejuni small RNAs. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b3880517
Abstract
Campylobacter jejuni (C. jejuni) is a zoonotic pathogen responsible for millions of bacterial gastroenteritis cases each year worldwide. The World Health Organisation (WHO) has also highlighted Campylobacter as one of the pathogens with high priority for research due to its emerging antibiotic resistance. One remarkable feature of C. jejuni is its persistence under various environmental stresses throughout transmission. However, very little is known about its genetic regulatory network. Annotation of the C. jejuni genome has only identified three sigma factors, suggesting additional regulatory mechanisms.
One potential regulatory element that requires further investigation is small RNA (sRNA). Studies in other pathogens have shown sRNA mediates post-transcriptional regulation by affecting translation initiation and mRNA stability, regulating processes involved in stress survival, virulence and antibiotic resistance. However, experimental discovery of C. jejuni sRNA is hindered by its fastidious nature and difficulties of experimental investigation. Several published transcriptomic studies on C. jejuni have discovered relatively few sRNAs, with limited insights into their biological activities. Moreover, most published RNA-seq data were obtained from standard laboratory conditions, limiting the exploration of stress adaptation by sRNAs.
This study aims to elucidate the condition-specific expression and activities of C. jejuni sRNAs. sRNA prediction was carried out using multiple tools that detect sRNA positions from genomic and transcriptomic data. The prediction produced a list of putative sRNAs. Further analysis of putative sRNA binding targets was carried out using in-house transcriptomic data, including 21 experimental conditions and aids in understanding sRNA activities under non-standard conditions. The bioinformatics analysis has generated a global sRNA-target regulatory network, followed by a detailed analysis of sRNAs related to food storage conditions and iron stress. In order to complement the limitations of bioinformatics prediction, sRNA-target interactions were identified experimentally using RNA crosslinking. The results have identified interactions that are absent from the computational prediction. The difference between RNA crosslinking and computational prediction may indicate different sRNA-regulatory mechanisms. Overall, this study has highlighted RNA-RNA interactions for future detailed analysis. xvii
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics Q Science > QP Physiology Q Science > QR Microbiology |
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Library of Congress Subject Headings (LCSH): | Campylobacter jejuni, Campylobacter jejuni -- Effect of stress on, Non-coding RNA, Campylobacter infections, Genetic transcription, Proteins -- Crosslinking | ||||
Official Date: | April 2022 | ||||
Dates: |
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Institution: | University of Warwick | ||||
Theses Department: | Warwick Medical School | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Constantinidou, Chrystala ; Alam, Tauqeer | ||||
Format of File: | |||||
Extent: | xvii, 279 pages : illustrations (some colour), charts | ||||
Language: | eng |
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