PROJECT SUMMARY/ ABSTRACT
An Epithelial to mesenchymal transition (EMT) is an essential program in many developmental
processes including gastrulation, neural crest formation, and myogenesis. EMT is a complex
morphogenetic event and, as such, is governed by groups of genes functioning as a gene
regulatory network (GRN). Through recent advances in many species we have begun to
understand the gene regulatory networks that regulate EMT. However, we still lack information
about how these networks function in detail. This is due in part to the slow nature of GRN
construction in which a major bottleneck is the identification of cis-regulatory elements. We
propose to overcome these limitations and apply novel high throughput methods to
construct the first high-resolution gene regulatory network of EMT. The sea urchin embryo
represents a unique opportunity to derive such a gene regulatory network of EMT. The EMT of
mesenchymal cells in the early sea urchin embryo is predictable, synchronous, and occurs in a
transparent embryo. Furthermore, gene regulatory networks describing germ layer specification
have been well established in the sea urchin. We propose to build on this knowledgebase and
apply new methods in high-throughput network construction to derive a high-resolution gene
regulatory network of EMT. This goal will be pursued as two specific aims. In the first aim, we
evaluate novel nodes that have been identified using co-expression network analysis. The
second aim seeks to use high throughput identification of cis-regulatory elements to identify the
EMT network wiring. These aims capitalize on the advanced state of knowledge of EMT and
embryonic gene regulatory networks of sea urchin.