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.identifier.uri |
http://hdl.handle.net/1794/19234 |
|
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.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.name |
Ph.D. |
|
thesis.degree.level |
doctoral |
|
thesis.degree.discipline |
Department of Biology |
|
thesis.degree.grantor |
University of Oregon |
|