Mortazavi, Ali (2008) Structure and evolution of mammalian gene networks. Dissertation (Ph.D.), California Institute of Technology. http://resolver.caltech.edu/CaltechETD:etd-05292008-140438
Accurate measurements of protein:DNA and RNA expression levels are critical to building meaningful models of gene regulatory networks. We develop here two new techniques doing such measurements using ultra-high-throughput DNA sequencing combined with extensive computational analyses, which we call respectively ChIP-seq and RNA-seq. To show the power and versatility of these techniques, we apply them to the study of two model problems that are representative of the research agenda of regulatory biology. We use ChIP-seq to study the conservation and evolution of the binding repertoire of the transcription factor NRSF/REST in boreoeutherian mammals, whereas we use ChIP-seq of RNA Polymerase II phosphoisoforms and RNA-seq to study a developmental time course of myogenesis in the C2C12 mouse cell line. Together, ChIP-seq and RNA-seq show the promise of ultra-high-throughout sequencing in mapping and studying gene regulatory networks which will likely supplant the previous generation of microarray-based technologies as the new generations of sequencers mature and become more generally available.
|Item Type:||Thesis (Dissertation (Ph.D.))|
|Subject Keywords:||ChIP-seq; ChIPSeq; CTD; NRSE; NRSF; polymerase; REST; RNA-seq; ultra-high-throughput|
|Degree Grantor:||California Institute of Technology|
|Thesis Availability:||Restricted to Caltech community only|
|Defense Date:||15 May 2008|
|Default Usage Policy:||No commercial reproduction, distribution, display or performance rights in this work are provided.|
|Deposited By:||Imported from ETD-db|
|Deposited On:||02 Jun 2008|
|Last Modified:||26 Dec 2012 02:49|
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