Gene expression levels are determined by the transcription rate of each gene and the decay rate of the resulting mRNA. The balance between these two processes can be altered in response to physiologic conditions, developmental signals, or disease states. Regulation of mRNA decay is particularly important in the nervous system, where the unique structure of neurons requires mRNAs to be selectively stabilized in axon terminals, far from their site of synthesis, and the generation of cellular diversity by neural progenitors requires the programmed decay of mRNAs that regulate proliferation or differentiation. Defective regulation of mRNA decay has been implicated in several human neurological disorders, including Alzheimer's disease and amyotrophic lateral sclerosis. To completely understand the role of mRNA decay in neural development and disease, it will be useful to construct mRNA decay regulatory networks that contain the following information: genome-wide mRNA decay rates in specific cell types under defined conditions, the regulatory proteins that target specific mRNAs for decay, and the mRNA sequence elements that confer coordinate programs of decay. To identify the components of such a network, it is necessary to measure mRNA decay in specific cell types, on a genome-wide scale, under in vivo conditions. Such experiments have historically been difficult, if not impossible, to perform. This project uses a novel technique, known as TU-tagging, that allows mRNA decay measurements from specific cell types under in vivo conditions. We have recently developed this technique in the model organism, Drosophila melanogaster, and are now well poised to use TU-tagging to identify mRNA decay regulatory networks in the Drosophila nervous system. Our aims are to optimize and validate the accuracy and sensitivity of TU-tagging-based mRNA decay measurements, measure mRNA stability in cells of the Drosophila nervous system, identify the mRNA targets of an mRNA decay regulatory factor encoded by the found in neurons (FNE) gene, and identify cis-regulatory elements among coordinately regulated mRNAs. The specific aims of this work encompass both technical goals and biological goals, reflecting the potential of this project to make significant contributions to the scientific toolkit as well as advance the understanding of fundamental biological processes that are relevant to human neural development and disease. PUBLIC HEALTH RELEVANCE: The development and function of the nervous system requires precise control of gene expression and the decay of messenger RNAs (mRNAs) is an essential yet often overlooked control mechanism. Altered regulation of mRNA decay has been implicated in developmental defects and neurological disorders, including Alzheimer's disease and amyotrophic lateral sclerosis. We have developed a novel technology that will allow genome-wide analysis of mRNA decay in neural cells and the construction of comprehensive blueprints of mRNA decay pathways that control nervous system development and function.