The rogue transcriptome : using sequencing to track RNA regulation and identify unusual RNAs
Abstract/Contents
- Abstract
- First, we take a look at the function of a specific type of RNA editing mediated by ADAR (adenosine deaminase that acts on RNAs). We test our hypotheses on ADAR activity and target specificity through transcriptome analysis in the context of exogenous RNAi response pathway in C. elegans. By examining of small RNA and mRNA populations in adar mutants and additional RNAi defective mutants, we show that the activity and specificity of the ADAR enzyme likely precludes the detection of its targets through conventional methods of sequence capture and analysis. Based on this understanding, we develop novel computational approaches for analysis of small RNA and mRNA populations and identify a broader set of ADAR targets, leading to a deeper understanding of the ADAR pathway, the conserved functionalities of the ADAR enzyme, and its relationship with the exogenous RNAi pathway in C. elegans. Second, we examine the dynamics of the transcriptome upon and after exposure to extreme heat. We hypothesize that the recovery response after removal from heat exposure might involve alternations in transcription regulation that are more complex than a reversal of the heat-shock induced effects, and that one such form of long-term regulation might involve the endogenous RNAi pathway and regulation via synthesis of endogenous siRNAs. By examining the dynamics of the C. elegans transcriptome during time-course of heat exposure and recovery, we reach a deeper understanding of heat shock biology and explore the relationship between endogenous siRNAs and their sequence complementary mRNA targets in the context of environmentally induced perturbance.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2013 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Wu, Di | |
|---|---|---|
| Associated with | Stanford University, Department of Genetics. | |
| Primary advisor | Fire, Andrew Zachary | |
| Thesis advisor | Fire, Andrew Zachary | |
| Thesis advisor | Kim, Stuart | |
| Thesis advisor | Montgomery, Stephen, 1979- | |
| Thesis advisor | Sidow, Arend | |
| Advisor | Kim, Stuart | |
| Advisor | Montgomery, Stephen, 1979- | |
| Advisor | Sidow, Arend |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Di Wu. |
|---|---|
| Note | Submitted to the Department of Genetics. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2013. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2013 by Di Wu
- License
- This work is licensed under a Creative Commons Attribution Non Commercial Share Alike 3.0 Unported license (CC BY-NC-SA).
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