The Life Cycle of the Intron: What Rare Splicing Intermediates Can Teach Us About Pre-mRNA Processing and Gene Expression

Taggart, Allison Jordan

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Year:: 2018
Contributor:: Taggart, Allison Jordan (creator); Fairbrother, William (Advisor); Reenan, Robert (Reader); Neretti, Nicola (Reader); Freiman, Richard (Reader); Pleiss, Jeffrey (Reader); Brown University. Department of Molecular Biology, Cell Biology and Biochemistry (sponsor)
Genre:: theses
Subject:: RNA sequencing; Bioinformatics; RNA; RNA splicing
Extent:: 19, 222 p.
DOI: https://doi.org/10.26300/cjvt-1a70

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Abstract:: Pre-mRNA splicing is an RNA processing step in which introns are excised and exons are ligated together. In this work, I use novel algorithms to probe RNA sequencing datasets with an intron-centric perspective. Using k-mer analysis and secondary structure prediction, a class of highly structured introns is discovered that form bridging structures to enforce correct splice site pairing and bypass the requirement for core splicing factor U2AF2. To study branch site usage in the first step of splicing, I developed a novel algorithm for mapping branchpoints in RNA sequencing data. This algorithm uses an iterative, inverted alignment approach to provide precise branchpoint sequence and position data. Applying this method, I produced the first genome-wide mapping of human branchpoints. From this data I was able to identify novel U2:pre-mRNA interactions and elucidate potential mechanisms relating branch site usage to alternate splicing outcome. To study lariat metabolism, I developed a second algorithm, ShapeShifter, which estimates abundance levels of individual lariats in a cell. Using ShapeShifter, I identified sets of apparent stabilized lariats under different RNAseq conditions. Herpes simplex 1 virus contains a stable lariat that is the dominant viral product produced during viral latency. I discover a second HSV1 lariat in the ICP0 gene, which is produced during viral lytic stage. Additionally I find that host cellular lariats increase under viral infection, and provide insight into potential roles for lariat metabolism in viral immunity.
Notes:: Thesis (Ph. D.)--Brown University, 2018

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Rights: In Copyright
Restrictions on Use: Collection is open for research.

Citation

Taggart, Allison Jordan, "The Life Cycle of the Intron: What Rare Splicing Intermediates Can Teach Us About Pre-mRNA Processing and Gene Expression" (2018). Molecular Biology, Cell Biology, and Biochemistry Theses and Dissertations. Brown Digital Repository. Brown University Library. https://doi.org/10.26300/cjvt-1a70

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Molecular Biology, Cell Biology, and Biochemistry Theses and Dissertations

Theses and Dissertations for the Molecular Biology, Cell Biology, and Biochemistry department.
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