PROJECT SUMMARY Decades of research have established that gene expression in the nervous system is highly specific and dynamic. Different types of neurons express dramatically different genes and process RNAs to generate different isoforms. At each developmental stage, neurons express complements of RNA that together drive them along appropriate trajectories toward their ultimate fate. Similarly, in mature neurons, differential gene expression and processing are key determinants of structure, function, and disease susceptibility. However, although these phenomena are well established, a deep and broad analysis—involving genome-wide, nervous system-wide data—is not available for any organism. Ideally one would like to know, across all neuron types and all developmental stages, exactly how the genome is transcribed and processed into functional RNAs. Such detailed and complete knowledge of differential gene expression within the nervous system would help elucidate the logic and cellular mechanisms that generate neuronal diversity. Further, by comparing dynamic differential gene expression across different sexes in all neuron types, the genetic basis of neuronal sexual dimorphism can be elucidated. The C. elegans Neuronal Gene Expression Map & Network (CeNGEN) project is a multi-lab consortium with the goal of understanding gene expression in the C. elegans nervous system. Here, using a variety of RNAseq approaches, we propose to understand gene expression as neurons differentiate and acquire sexual dimorphisms for every neuron type in the C. elegans nervous system, with these Aims: Aim 1) Build and analyze a gene expression atlas for every neuron type at each stage of the developmental lineage. Aim 2) Develop a gene expression atlas across sexes, identifying sexually dimorphic gene expression in sex-shared neurons, as well as gene expression in sex-specific neurons. Aim 3) Describe splicing patterns for all genes and all neuron types, and use this information to identify all instances of differential alternative splicing. Aim 4) Generate and distribute analysis tools and data to the scientific community. CeNGEN represents a paradigmatic advance in neurogenetics, and provides a unique opportunity to elucidate the global control of neuron-specific gene expression and to relate developmental gene expression and splicing to ultimate neuronal wiring and function. CeNGEN will also serve as a resource for future studies in C. elegans neuroscience, and will provide a framework for addressing global differential gene expression in more complex nervous systems that are currently not amenable to this comprehensive approach.