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Ribosome Profiling of EBV-infected cells

Bencun, Maja

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Abstract

The Epstein-Barr-Virus is an oncogenic herpesvirus that establishes a lifelong infection in humans. It is ubiquitous in the population and is responsible for the development of multiple diseases including cancer. Analysis of the EBV DNA and RNA sequences has predicted that the viral genome encodes approximately 100 protein-coding genes. However, the existence of many putative proteins has not been confirmed by biochemical methods yet. Furthermore, the identification of EBV open reading frames (ORFs) is difficult as viral genes are encoded on both strands of the double-stranded DNA genome and often overlap. Moreover, EBV encodes different types of non-coding RNAs. In order to identify the full scope of EBV’s coding capacity, ribosome profiling of replicating and non-replicating EBV strains was performed. Ribosome profiling combines classical ribosome footprinting experiments with current deep sequencing technology to map translating ribosomes on mRNA at single nucleotide resolution. This approach confirmed the majority of previously identified ORFs and has enabled the identification of 28 novel small open reading frames and of 8 alternative translation initiation sites. 25 of the 28 small ORFs were localized in the 5’leaders of several mRNA transcripts and are classified as upstream open reading frames (uORFs). Several of these uORFs were found to repress the translation of the downstream encoded main ORF. In summary, ribosome profiling of EBV-infected cells has allowed a comprehensive identification and annotation of the EBV ORFs and has revealed a novel mode of viral gene expression regulation at the translational level.

Item Type: Dissertation
Supervisor: Müller, Prof. Dr. Martin
Place of Publication: Heidelberg
Date of thesis defense: 9 December 2016
Date Deposited: 01 Jun 2017 08:22
Date: 2017
Faculties / Institutes: The Faculty of Bio Sciences > Dean's Office of the Faculty of Bio Sciences
Subjects: 500 Natural sciences and mathematics
570 Life sciences
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