Author's School

Graduate School of Arts & Sciences

Author's Department/Program

Biology and Biomedical Sciences: Molecular Genetics and Genomics


English (en)

Date of Award

January 2010

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Mark Johnston


Gene expression is an elaborate and finely tuned process involving the regulated interactions of multiple proteins with promoter and enhancer elements. A variety of approaches are currently used to study these interactions in vivo, in vitro as well as in silico. With the genome sequences of many organisms now readily available, a plethora of DNA functional elements have been predicted, but the process of identifying the proteins that bind to them in vivo remains a bottleneck. I developed two high-throughput assays to address this issue. The first is a modification of the yeast "one-hybrid" assay. The second is probing protein microarrays with DNA sequence elements. Using these methods, I identified two proteins, Sef1 and Yjl103c, that bind to the same DNA sequence element. Sef1 and Yjl103c are little-characterized members of the zinc cluster family of transcription factors of S. cerevisiae. Characterization of their mechanism of action as well as identification of some of their target genes leads to the conclusion that they play a pivotal role in the transcriptional regulation of utilization of nonfermentable carbon sources by budding yeast.


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