PROJECT SUMMARY/ABSTRACT Chromatin can be characterized by proximity to membraneless nuclear compartments such as the lamina, which is associated with repressive heterochromatin, or speckles, which facilitate mRNA splicing. Many genomic regions spanning tens to hundreds of kilobases interact with these nuclear compartments. This level of genome organization is regulated and provides a 3-dimensional (3D) architecture for transcriptional regulation. Nuclear compartment-associated genome organization in post-mitotic, mature neurons is not known, and emerging evidence indicate that nuclear compartments are grossly perturbed in a wide range of neurodegenerative diseases including Alzheimer’s disease (AD). Recently, a new technique called Genome Organization with Cut and Run Technology (GO-CaRT) was developed to identify chromatin domains in proximity to specific nuclear compartments – the nuclear lamina (lamina associated domains, LADs), and nuclear speckles (speckle associated domains, SPADs) – in cells isolated from mouse and human brain. In human neural precursor cells, SPADs are enriched for genes involved in microtubule-based movement, suggesting that speckles regulate ongoing key cellular processes. In other Preliminary Studies, SPADs were found to be highly enriched for known AD risk loci. Tauopathies are progressive, neurodegenerative diseases defined by insoluble tau aggregates in the brain. Multiple studies have demonstrated that key speckle proteins become mislocalized to aggregates of pathogenic tau, severely disrupting the structure of nuclear speckles. Based on this scientific background and Preliminary Studies, the central hypothesis of this proposal is that the mislocalization of speckle proteins to tau aggregates in tauopathies leads to loss of speckle-association of key neuronal genes, which results in defects in their transcription and splicing. To test this hypothesis, Aim 1 will elucidate the maturation of genome organization in healthy, post-mitotic cortical neurons in the mouse using GO-CaRT and related epigenomic and transcriptomic methods. Aim 2 will then investigate effect of tau aggregates on genome architecture, using established animal models of pathogenic tau expression. Successful completion of these Aims will elucidate the relationship between gene regulation and nuclear compartment-associated genome organization in neurons in vivo. Results will also provide insights into how disruption of nuclear compartments in tauopathies can contribute to aberrant gene expression and splicing, potentially generating new models of the pathogenesis of tauopathies such as AD. From a training perspective, this proposal compliments the applicant’s past experience with bioinformatics/computational biology with training in “wet lab” molecular biology and animal models of human neurological disease. Providing training in these aspects of experimental biology will be invaluable to the applicant’s career interests in neurology and neurodegene...