A study of mRNA translation with computational analysis of ribosome profiling datasets

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O'Connor, Patrick
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University College Cork
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Ribosome profiling is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a “snapshot” of ribosome positions at the transcriptome wide level. The approach was developed in 2009 and was a significant advancement towards the better understanding of the regulation of protein synthesis. I this thesis I describe my analysis of ribosome profiling data. In Chapter 1, I present a review of the recent developments of understanding obtained with ribosome profiling as well as discussing the implications of artifacts on the interpretation of its data. Chapters 2 and 3 details using ribosome profiling to examine the translational response to eIF2 repression and to the deprivation of oxygen and glucose respectively. Chapter 4 details how the interaction of the Shine Dalgarno with the ribosome rRNA alters the length of the mRNA protected fragments. In Chapter 5, I present analysis at identifying the relative impact of mRNA features on local ribosome profiling read density.
Translation , Ribosome profiling
O'Connor, P. 2017. A study of mRNA translation with computational analysis of ribosome profiling datasets. PhD Thesis, University College Cork.