CONSTRUCTING A HIGH-RESOLUTION GENE REGULATORY NETWORK OF EMT

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.