Show simple item record

dc.contributor.advisor Ohler, Uwe en_US
dc.contributor.author Rach, Elizabeth Ann en_US
dc.date.accessioned 2010-05-10T20:17:28Z
dc.date.available 2012-05-01T04:30:05Z
dc.date.issued 2010 en_US
dc.identifier.uri http://hdl.handle.net/10161/2454
dc.description Dissertation en_US
dc.description.abstract <p>Transcription initiation is a key component in the regulation of gene expression. Recent high-throughput sequencing techniques have enhanced our understanding of mammalian transcription by revealing narrow and broad patterns of transcription start sites (TSSs). Transcription initiation is central to the determination of condition specificity, as distinct repertoires of transcription factors (TFs) that assist in the recruitment of the RNA polymerase II to the DNA are present under different conditions. However, our understanding of the presence and spatiotemporal architecture of the promoter patterns in the fruit fly remains in its infancy. Nucleosome organization and transcription initiation have been considered hallmarks of gene expression, but their cooperative regulation is also not yet understood.</p> <p>In this work, we applied a hierarchical clustering strategy on available 5' expressed sequence tags (ESTs), and developed an improved paired-end sequencing strategy to explore the transcription initiation landscape of the D.melanogaster genome. We distinguished three initiation patterns: 'Peaked or Narrow Peak TSSs&#8219;, 'Broad Peak TSSs&#8219;, and 'Broad TSS cluster groups or Weak Peak TSSs&#8219;. The promoters of peaked TSSs contained the location specific sequence elements, and were bound by TATA Binding Protein (TBP), while the promoters of broad TSS cluster groups were associated with non-location-specific elements, and were bound by the TATA-box related Factor 2 (TRF2).</p> <p>Available ESTs and a tiling array time series enabled us to show that TSSs had distinct associations to conditions, and temporal patterns of embryonic activity differed across the majority of alternative promoters. Peaked promoters had an association to maternally inherited transcripts, and broad TSS cluster group promoters were more highly associated to zygotic utilization. The paired-end sequencing strategy identified a large number of 5' capped transcripts originating from coding exons that were unlikely the result of alternative TSSs, but rather the product of post-transcriptional modifications.</p> <p>We applied an innovative search program called FREE to embryo, head, and testes specific core promoter sequences and identified 123 motifs: 16 novel and 107 supported by other motif sources. Motifs in the embryo specific core promoters were found at location hotspots from the TSS. A family of oligos was discovered that matched the Pause Button motif that is associated with RNA pol II stalling.</p> <p>Lastly, we analyzed nucleosome organization, chromatin structure, and insulators across the three promoter patterns in the fruit fly and human genomes. The WP promoters showed higher associations with H2A.Z, DNase Hypersensitivity Sites (DHS), H3K4 methylations, and Class I insulators CTCF/BEAF32/CP190. Conversely, NP promoters had higher associations with polII and GAF binding. BP promoters exhibited a combination of features from both promoter patterns. Our study provides a comprehensive map of initiation sites and the conditions under which they are utilized in D. melanogaster. The presence of promoter specific histone replacements, chromatin modifications, and insulator elements support the existence of two divergent strategies of transcriptional regulation in higher eukaryotes. Together, these data illustrate the complex regulatory code of transcription initiation.</p> en_US
dc.format.extent 6566125 bytes
dc.format.mimetype application/pdf
dc.language.iso en_US
dc.subject Biology, Genetics en_US
dc.subject core promoter en_US
dc.subject Drosophila melanogaster en_US
dc.subject histone variants en_US
dc.subject spatial regulation en_US
dc.subject temporal regulation en_US
dc.subject transcription en_US
dc.title The Spatial and Temporal Regulatory Code of Transcription Initiation in Drosophila melanogaster en_US
dc.type Dissertation en_US
dc.department Computational Biology and Bioinformatics en_US
duke.embargo.months 24 en_US

Files in this item

This item appears in the following Collection(s)

Show simple item record