Understanding the response of gene networks to environmental perturbation
Abstract/Contents
- Abstract
- Large-scale screens of genetic interactions (GIs) in Saccharomyces cerevisiae have been a crucial tool for both defining overall cellular network topology and characterizing novel gene function. However, most screens have been limited to characterizing gene interaction networks in a single environment. Moving beyond this static view of the cell requires a major technological advance to increase the throughput and ease of replication in these assays. Here, I develop and apply two novel pooled screening methodologies for conditional measurements of genetic interactions. Both approaches utilize DNA double-barcoding systems, coupled with amplicon sequencing, to estimate fitness in a highly parallel fashion. These screens of up to 17,000 double-barcoded mutant strains, in up to five growth conditions, illustrate that conditional measurements can increase the number of observed interactions by 3-fold. Furthermore, statistical methods implemented on these datasets support the hypothesis that functional classification using GI screening data is improved by assaying more conditions. Finally, new links during respiratory growth between Ras-nutrient sensing pathway members are found with both the COG complex and a gene of unknown function. Together, this work provides key insights into how the gene network changes upon environmental perturbation and establishes the technology for future studies to further expand our knowledge in this domain.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2017 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Jaffe, Mia |
|---|---|
| Associated with | Stanford University, Department of Genetics. |
| Primary advisor | Sherlock, Gavin |
| Thesis advisor | Sherlock, Gavin |
| Thesis advisor | Bassik, Michael |
| Thesis advisor | Pringle, John R, 1943- |
| Thesis advisor | Skotheim, Jan |
| Advisor | Bassik, Michael |
| Advisor | Pringle, John R, 1943- |
| Advisor | Skotheim, Jan |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Mia Jaffe. |
|---|---|
| Note | Submitted to the Department of Genetics. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2017. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2017 by Mia Jaffe
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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