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Tackling the regulatory genome


Brown, Charles Titus (2007) Tackling the regulatory genome. Dissertation (Ph.D.), California Institute of Technology.


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
Author Email:ctb (AT)
Record Number:CaltechETD:etd-12192006-100331
Persistent URL:
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:12 Mar 2013 21:20

Thesis Files

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