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Date of Award
Doctor of Philosophy (PhD)
The ability to create distinct cell types is fundamental for the development of multicellular organisms. Since all cells in an organism contain the same genes, cellular diversity is achieved through the transcriptional network where transcription factors (TFs) interacts with cis-regulatory elements, leading to the selective transcription of different sets of genes. To better understand the functions of TFs and regulatory elements underlying cell fate decisions, we developed methods that are able to record their activities throughout cellular differentiation. In Chapter 2, we developed a degradation domain based induction system for ҃alling CardsӠmethod which maps the binding sites of TFs using piggybac transposons. The induction ҃alling CardsӠmethod offers an alternative to chromatin immunoprecipitation (ChIP) methods and furthermore has the ability to record TF binding at different time periods of the development. In Chapter 3, we applied the ҃alling CardӠmethod to study the role of master regulatory Brd4-bound enhancers for sex differences in glioblastoma. We revealed a set of sex-specific regulatory genes and networks, which are indicative of sex-specific transcriptional programs regulated by Brd4-bound enhancers. Finally, to record the activity of regulatory elements or enhancers, in Chapter 4, we developed a CRE recombinase-mediated method for high-throughput functional identification of active enhancers at different time periods of the development, named as Developmental Enhancer Sequencing (DevEn-seq). We demonstrated that DevEn-seq is able to detect enhancers more efficiently than regular reporter methods and trace enhancer activities throughout cellular differentiation without being disturbed by the gene silencing effect caused by lentiviral sequences. With an in vitro neural differentiation protocol, we identified two neural progenitor-specific enhancers near HB9 and Olig2 genes respectively. In summary, this dissertation contributes to the field of developmental biology by providing useful methods for recording TF binding events and enhancer activities throughout development.
Chair and Committee
Robi D. Mitra
Barak A. Cohen, Joseph D. Dougherty, Joshua B. Rubin, Gary D. Stormo,
Qi, Zongtai, "Methods to Record Transcription Factor Binding and Enhancer Activity throughout Cellular Differentiation" (2018). Arts & Sciences Electronic Theses and Dissertations. 1647.
Available for download on Monday, August 24, 2020