BME PhD Prospectus Defense - Patricia Aquino
- Starts: 1:00 pm on Tuesday, December 12, 2017
Title: “Characterization of transcription factor binding interactions in bacteria” Committee: James Galagan, PhD – BME (Adviser, Chair) Wilson Wong, PhD – BME Thomas Tullius, PhD – Chemistry David Waxman, PhD – Biology Abstract: Bacterial transcription factors (TFs) enable gene regulation by recognizing and binding regulatory DNA sequences and subsequent recruitment of transcriptional machinery. The emergence of new genomic techniques has made global mapping of TF-DNA binding sites more feasible. The advent of next-generation sequencing (NGS) methods such as chromatin immunoprecipitation followed by sequencing (ChIP-Seq) provides high-resolution genome wide binding data that helps increase our understanding of bacterial gene regulatory networks. This technology has only been applied on a handful of bacterial TFs, leading to more transcription factor binding sites (TFBS) open for discovery. However, data generated from ChIP-Seq analysis has shown poor correlation with TF-DNA binding motif predictions. In order to address the differences observed in genome wide TF binding data against predicted binding sites, we develop a high-throughput in vitro ChIP-Seq method that will produce a complementary data set used for comparison of TF binding across in vivo and in vitro conditions. Integration of in vivo and in vitro binding data in the assessment of TF binding patterns across the genome can lead to better characterization of TF behavior in the cell.
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