Analysis of a Model Developmental Gene Regulatory Network

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Multicellular organisms arise from a single cell- a fertilized egg- through a process known as embryonic development. During this process, 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 great scientific importance, as this is the process by which new generations of multicellular organisms arise. Moreover, during earth’s history, modifications to developmental programs have produced the diverse animal morphologies we see in nature. Lastly, failures of human development have profound societal impacts, and any appreciation of the causes of such dysregulation must begin with an understanding of the mechanisms that ordinarily operate during development. 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 genomic information is “decoded” to control the process of embryogenesis. This research project addresses that question. It exploits new methods (and undergraduate researchers) for examining the physical structure of genomic DNA, for monitoring when and where in the embryo various genes are working, and for dissecting interactions among these genes. The work will shed light on the mechanisms by which the information contained in the genome is deciphered during the transformation of a single cell into an organism, and will form a foundation for development of a digital atlas of echinoderm development. A hallmark of animal development is the gradual emergence of anatomy, as represented by the many different cell types of the mature organism and their organization into distinct tissues and organs. The emergence of anatomy during embryonic development (morphogenesis) requires specialized cell and tissue behaviors that are driven by differential gene expression. Systems level approaches have revealed that programs of differential gene expression are controlled by complex networks of transcription factors and non-coding DNA sequences to which they bind. Such gene regulatory networks (GRNs) are powerful tools for analyzing the genetic control and evolution of development. To understand the genotype-to-phenotype transformation it will therefore be important to link GRNs to morphogenesis. The overarching goal of this work is to uncover the detailed architecture of a model GRN and elucidate its control of crucial downstream effectors that drive morphogenesis. It leverages a GRN that drives a suite of spectacular behaviors by skeleton-forming primary mesenchyme cells (PMCs) of the sea urchin embryo. The project combines “top-down” and “bottom-up” approaches. The former uses gene knockdowns and gene expression profiling to elucidate the regulatory topology of the network. The latter uses chromatin accessibility profiling and eRNA analysis to identify cis-regulatory DNA sequences that control morphogenetic effector genes, and then applies transcription factor footprinting, mutagenesis, and transgenic reporter assays to dissect these sequences and bootstrap into the upstream network circuitry. Lastly, the project extends a successful gene knockdown screen to identify and characterize key morphogenetic effectors. With respect to Broader Impacts, this project involves undergraduate researchers, outreach to high school students and teachers, and the development of a digital atlas of echinoderm development.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.