Identifying locations and characterizing cis regulation of RNA editing
Abstract/Contents
- Abstract
- A-to-I RNA editing is an important post-transcriptional gene regulatory process. However, the field has been vastly understudied. Only recently have technologies emerged that can evaluate RNA editing transcriptome-wide. This dissertation provides insights into the abundance of RNA editing in the transcriptome and how this editing process is regulated in cis. In chapter 2, I describe a bioinformatics pipeline developed to accurately identify RNA editing sites from matched RNA and genomic DNA sequencing. In chapter 3, I extend the pipeline developed in chapter 2 to identify RNA editing sites using RNA sequencing data by itself. In chapter 4, I measure how RNA editing varies across a population of Drosophila melanogaster and identify genetic variants associated with changes in editing. In chapter 5, I extended the analyses in chapter 4 to human data from the GTEx project as well as develop a synthetic biology approach to systematically perturb editing substrates and finely characterize how changes in RNA structure affect RNA editing.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2015 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Ramaswami, Gokul |
|---|---|
| Associated with | Stanford University, Program in Genetics. |
| Primary advisor | Li, Jin |
| Thesis advisor | Li, Jin |
| Thesis advisor | Fraser, Hunter B |
| Thesis advisor | Kim, Stuart |
| Thesis advisor | Montgomery, Stephen, 1979- |
| Advisor | Fraser, Hunter B |
| Advisor | Kim, Stuart |
| Advisor | Montgomery, Stephen, 1979- |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Gokul Ramaswami. |
|---|---|
| Note | Submitted to the Program in Genetics. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2015. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2015 by Gokul Ramaswami
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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