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Tackling the Regulatory Genome


Brown, Charles Titus (2007) Tackling the Regulatory Genome. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/STPG-0P56.


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.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:cis-regulation; comparative sequence analysis; gene regulation
Degree Grantor:California Institute of Technology
Major Option:Biology
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Davidson, Eric H.
Thesis Committee:
  • Sternberg, Paul W. (chair)
  • Wold, Barbara J.
  • Adami, Christoph Carl
  • Davidson, Eric H.
  • Fraser, Scott E.
Defense Date:5 September 2005
Non-Caltech Author Email:ctb (AT)
Record Number:CaltechETD:etd-12192006-100331
Persistent URL:
Brown, Charles Titus0000-0001-6001-2677
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:5063
Deposited By: Imported from ETD-db
Deposited On:26 Mar 2007
Last Modified:19 Feb 2020 18:43

Thesis Files

PDF (thesis-final-mar23-07.pdf) - Final Version
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