University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Killing The Messenger: Exploring Novel Triggers For Messenger Rna Decay In Eukaryotes Lee Elliott Vandivier University of Pennsylvania,
[email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Biology Commons, and the Genetics Commons Recommended Citation Vandivier, Lee Elliott, "Killing The Messenger: Exploring Novel Triggers For Messenger Rna Decay In Eukaryotes" (2017). Publicly Accessible Penn Dissertations. 2621. https://repository.upenn.edu/edissertations/2621 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2621 For more information, please contact
[email protected]. Killing The Messenger: Exploring Novel Triggers For Messenger Rna Decay In Eukaryotes Abstract The lifecycle of messenger RNAs is regulated by multiple layers beyond their primary sequence. In addition to carrying the information for protein synthesis, mRNAs are decorated with RNA binding proteins, marked with covalent chemical modifications, and fold into intricate secondary structures. However, the full set of information encoded by these “epitranscriptomic” layers is only partially understood, and is often only characterized for select transcripts. Thus, it is crucial to develop and apply transcriptome-wide analytical tools to probe the location and functional relevance of epitranscriptome features. In this dissertation, I focus on applying such methods toward better understanding determinants of mRNA stability, through using 1) High Throughput Annotation of Modified Nucleotides, 2) nuclease- mediated probing of RNA secondary structure, and 3) detection of partial mRNA degradation from RNA sequencing. I observe that chemical modifications tend ot mark uncapped and small RNA fragments derived from mRNAs in plants and humans, suggesting a link between modifications and mRNA stability.