Tackling the Regulatory Genome

Author: Brown, Charles Titus

Year: 2007

Degree: Dissertation (Ph.D.)

Advisor: Davidson, Eric H.

Committee Members: Sternberg, Paul W.; Wold, Barbara J.; Adami, Christoph Carl; Davidson, Eric H.; Fraser, Scott E.

Option: Biology

DOI: 10.7907/STPG-0P56

Abstract

The structure of the gene regulatory networks that drive animal development is encoded in the genome in cis-regulatory regions. Locating these regions and understanding how they integrate regulatory information to produce specific spatiotemporal patterns of gene expression is a major challenge facing developmental biology. This thesis presents computational and experimental work on finding, dissecting, and understanding regulatory regions. I discuss the use of comparative sequence analysis or "phylogenetic footprinting" to locate regulatory regions in animals. I then present experimental work on dissecting the information encoded in the cyIIIa cis-regulatory system of the California purple sea urchin, Strongylocentrotus purpuratus. Finally, I present a computational investigation of binding site validation techniques in E.coli.

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