Analysis of a Model Developmental Gene Regulatory Network

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Non-Technical ParagraphIn development, multicellular organisms arise from a single cell - a fertilized egg. Repeated cell divisions create an embryo composed of many cells. These cells gradually take on distinct functions and organize themselves into tissues and organs. Understanding development is of cardinal scientific importance, as this is the process by which new generations of multicellular organisms arise. Remarkably, the entire blueprint for embryonic development is contained in the DNA sequence of the genome. A central challenge of modern biology is to explain how this genome information is "decoded" to control the process of development. The research project described here addresses this question, using the sea urchin embryo as a convenient experimental model. It examines the genes that encode the formation of the skeleton of these sea creatures through use of new methods to examine the physical structure of genomic DNA, to monitor when and where in the embryo various genes work, and to determine interactions among these genes. The work will shed light on the mechanisms by which the information contained in the genome is deciphered during the development of a single cell into a critical part of these organisms. Technical ParagraphThe central challenge of developmental biology is to link genes to anatomy. The programs of differential gene expression that drive development are largely controlled by complex networks of regulatory genes (i.e., genes that encode transcription factors, or TFs) and the non-coding DNA sequences to which TFs bind. Such gene regulatory networks (GRNs) are powerful tools for analyzing the genetic control and evolution of development. At present, we have a very limited understanding of the connections between GRNs and the processes that directly shape embryonic tissues and organs (morphogenesis). The project described here addresses this question using the sea urchin embryo, a pre-eminent system for both GRN biology and the analysis of morphogenesis. The project leverages one of the most complete GRNs in any developing organism, a GRN that drives a suite of cell behaviors by primary mesenchyme cells (PMCs) and culminates in the formation of the embryonic skeleton. The research plan takes a "top-down" approach to dissect the architecture of an essential subcircuit controlled by Alx1, a key TF in the skeletogenic GRN. These studies utilize gene knockdowns, mRNA overexpression, gene expression profiling, and bioinformatics-based approaches. In parallel, a "bottom-up" approach is taken that uses reporter gene assays to dissect non-coding regulatory DNA sequences that control the transcription of morphogenetic effector genes. This information is used to bootstrap into the upstream network circuitry. Lastly, the project extends a gene knockdown screen to identify and characterize new morphogenetic effectors that have emerged from genome-wide profiling of PMC-enriched transcripts and Alx1 targets.