DukeSpace will be down for maintenance at 9:15 AM EDT on Tuesday, July 29. Expected downtime is 20 minutes or less.

Show simple item record

dc.contributor.advisor Furey, Terrence S en_US
dc.contributor.author Boyle, Alan P en_US
dc.date.accessioned 2009-12-18T16:26:26Z
dc.date.available 2009-12-18T16:26:26Z
dc.date.issued 2009 en_US
dc.identifier.uri http://hdl.handle.net/10161/1634
dc.description Dissertation en_US
dc.description.abstract <p>Cis-elements govern the key step of transcription to regulate gene expression within a cell. Identification of utilized elements within a particular cell line will help further our understanding of individual and cumulative effects of trans-acting factors. These elements can be identified through an assay leveraging the ability of DNaseI to cut DNA that is in an open and accessible state making it hypersensitive to cleavage. Here we develop and explore computational techniques to measure open chromatin from sequencing and microarray data. We are able to identify 94,925 DNaseI hypersensitive sites genome-wide in CD4+ T cells. Interestingly, only 16%-20% of these sites were found in promoters. We also show that these regions are associated with different chromatin modifications. We found that DNaseI data can also be used to identify precise 'footprints' indicating protein-DNA interaction sites. Footprints for specific transcription factors correlate well with ChIP-seq enrichment, reveal distinct conservation patters, and reveal a cell-type specific arrangement of transcriptional regulation. These footprints can be used in addition to or in lieu of ChIP-seq data to better understand genomic regulatory systems.</p> en_US
dc.format.extent 6403836 bytes
dc.format.mimetype application/pdf
dc.language.iso en_US
dc.subject Biology, Bioinformatics en_US
dc.subject Biology, Molecular en_US
dc.subject chromatin en_US
dc.subject DNase en_US
dc.subject footprinting en_US
dc.subject regulation en_US
dc.title Studies on Human Chromatin Using High-Throughput DNaseI Sequencing en_US
dc.type Dissertation en_US
dc.department Computational Biology and Bioinformatics en_US

Files in this item

This item appears in the following Collection(s)

Show simple item record