Massively Parallel Sequencing-Based Analyses of Genome and Protein Function
| dc.contributor.advisor | Bowerman, Bruce | |
| dc.contributor.author | Kamps-Hughes, Nicholas | |
| dc.date.accessioned | 2015-08-18T23:00:33Z | |
| dc.date.available | 2015-08-18T23:00:33Z | |
| dc.date.issued | 2015-08-18 | |
| dc.description.abstract | The advent of high-throughput DNA and RNA sequencing has made possible the assay of millions of nucleic acid molecules in parallel. This allows functional genomic elements to be identified from background in single-tube experiments. This dissertation discusses the development of two such functional screens as well as work implementing a third that was previously developed in my thesis laboratory. Restriction-Associated DNA sequencing (RAD-Seq) is a complexity reduction sequencing method that allows the same subset of genomic sequence to be read across multiple samples. Differences in sample collection and data analysis allow manifold applications of RAD-Seq. Here we use RAD-Seq to identify mutant genes responsible for altered phenotypes in Caenorhabditis elegans and to identify hyper-invasive alleles in trout population admixtures. Apart from acquiring genomic sequence data, massively-parallel sequencing can be used for counting applications that quantify activity across a large number of test molecules. This dissertation describes the development of a technique for simultaneously quantifying the activity of a restriction enzyme across all possible DNA substrates by linking digest of a sequenced genome to Illumina-sequencing in an unbiased fashion. Finally, a powerful approach to analyze transcriptional activation is described. This method quantifies output from millions of potential DNA transcriptional enhancers via RNA amplicon sequencing of covalently-linked randomer tags and is used in conjunction with RNA-Seq to provide a mechanistic view of hypoxic gene regulation in Drosophila. This dissertation includes previously published, co-authored material | en_US |
| dc.identifier.uri | https://hdl.handle.net/1794/19234 | |
| dc.language.iso | en_US | |
| dc.publisher | University of Oregon | |
| dc.rights | All Rights Reserved. | |
| dc.subject | Gene regulation | en_US |
| dc.subject | Genomics | en_US |
| dc.subject | High-throughput sequencing | en_US |
| dc.subject | Population genetics | en_US |
| dc.subject | Restriction enzymes | en_US |
| dc.title | Massively Parallel Sequencing-Based Analyses of Genome and Protein Function | |
| dc.type | Electronic Thesis or Dissertation | |
| thesis.degree.discipline | Department of Biology | |
| thesis.degree.grantor | University of Oregon | |
| thesis.degree.level | doctoral | |
| thesis.degree.name | Ph.D. |
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