The Sea Urchin Regulome in Development

Citation

Ashby, Meredith Howard (2007) The Sea Urchin Regulome in Development. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/523T-5R49. https://resolver.caltech.edu/CaltechETD:etd-10192006-114144

Abstract

During development an organism undergoes many rounds of pattern formation, generating ever greater complexity with each ensuing round of cell division and specification. The instructions for executing this process are encoded in the DNA, in cis-regulatory modules that direct the expression of developmental transcription factors and signaling molecules. Each transcription factor binding site within a cis-regulatory module contributes information about when, where or how much a gene is turned on, and by dissecting the modules driving a given gene, all the inputs governing expression of the gene can be accurately identified. Furthermore, by mapping the output of each gene to the inputs of other genes, it is possible to reverse engineer developmental circuits and even whole networks, revealing common bilaterian strategies for specifying progenitor fields, locking down regulatory states, and driving development forward. The S. purpuratus endomesodermal gene network is one of the best-characterized developmental networks, with interactions between over 40 regulatory genes mapped by perturbation experiments. With the sequencing of the sea urchin genome, it is possible to move towards the definitive completion of this network. By identifying all the transcription factors in the genome and determining their expression patterns, any previously unrecognized players can be incorporated into the network. In addition, such a comprehensive examination of transcription factor usage in maximally indirect development has not been done and will itself yield interesting conclusions.

Thesis Files