regulatory networks of cell shape in Drosophila epidermis development and evolution – Netoshape

Morphological features characterize every animal species and their study had major impacts for the formulation of concepts in biology, for example evolutionary theories. Paradoxically, the mechanisms underlying the acquisition of animal forms during development, as well as evolutionary mechanisms, remain poorly understood. Numerous functional studies have demonstrated that regulatory networks play critical roles in cell specification and differentiation and thereby control morphogenesis during development. It is well established that gene regulatory networks are implemented by transcription factors that bind to cis-regulatory elements to regulate gene expression. However our understanding of the fine structure and logic of these networks is currently limited to a few cases and mostly remain unconnected to morphological differentiation. Experimental case studies support that modifications of cis-regulatory elements have an important part in the evolution of animal forms. However, cases of evolutionary diversification are not yet fully integrated within developmental networks. Therefore, a major challenge resides in deciphering the logic underlying developmental regulatory networks that are directly connected with evolutionary diversification. We aim to address this question through the analysis of a transcription factor, Shavenbaby, which controls a simple morphological trait during Drosophila development and was shown to underlie parallel evolution in insects. We have demonstrated that Shavenbaby directly controls the transcription of various cellular effectors, collectively responsible for the cell shape changes underlying epidermal differentiation and thus external morphology. Recently, we showed that modifications of the cis-regulatory elements governing Shavenbaby transcription are the unique cause of the morphological evolution that characterizes a sibling Drosophila species. Shavenbaby expression integrates various developmental inputs, including those emanating from the well know regulatory networks underlying embryonic segmentation, dorso-ventral patterning, as well as Hox genes. Therefore, elucidation of the mechanisms acting upstream and downstream of shavenbaby will offer the opportunity to connect upstream regulatory cascades to the effectors of cell shape control. Our goal is to provide a comprehensive understanding of this gene regulatory network and define functional consequences of its experimental and evolutionary modifications. This will be one of the first cases of molecular comprehension of a gene network controlling a morphological feature, therefore representing a significant advance to our general understanding of regulatory network structure and function during development and evolution. Our strategy is based on an integrated approach taking advantage of recent advances of genomic tools and knowledge in flies. It incorporates functional genomics, genome-wide identification of cis-regulatory elements from experimental and computational methods, and high throughput in vivo analyses. Preliminary results acquired in the lab and a network of collaboration with expert teams in their respective domain support the feasibility of our research program. In addition, it will directly benefit from high quality local technological resources (genomics and proteomics). Our specific aims are to: 1) Decipher how upstream regulatory cascades are functionally integrated to determine the pattern of cell morphogenesis. We will identify the cis-regulatory elements that govern expression of the shavenbaby transcription factor, analyze functional consequences of their modifications and identify upstream regulators. 2) Identify the whole set of cellular effectors responsible for cell shape changes and define variation of its composition between cells that display distinct morphologies. We will use ChipSeq to define the genome-wide distribution of shavenbaby binding sites and develop an approach to target this search in a given subpopulation of cells. 3) Uncover the cis-regulatory code underlying transcriptional regulation of cellular effectors. Iterations of computational prediction and in vivo tests will define the cis-regulatory elements that control expression of these cellular effectors. We will identify and analyze roles of additional DNA binding proteins and other molecules in the control of their transcription.