Gene and Chromatin Analysis Core

PROJECT SUMMARY/ABSTRACT – GENE AND CHROMATIN ANALYSIS CORE The Gene and Chromatin Analysis Core provides the technical and bioinformatics infrastructure to optimally mine the large amount of genome-wide gene expression and chromatin data that are generated from the PPG’s work. PPG investigators lead the field in several aspects of genome-wide analyses, including pioneering these approaches to specific cell types in brain, which offers several technical challenges. We use optimized methods for the most advanced sequencing approaches, including RNAseq, ChIPseq, CUT&RUN, ATACseq, HiC, and whole genome bisulfite sequencing, among others, for rodent and human brain, the latter offering an additional set of unique technical challenges. These approaches are being used increasingly to study individual cells within a given brain reward region as well as individual cells within intact tissue (spatial transcriptomics), in both rodent and human. The Core has established expertise in analyzing the highly complex datasets obtained, and works to further improve the tools available. All of the genome-wide data generated by our PPG are analyzed by this Core. In parallel, the Core runs routine genome-wide assays on defined animal models with the Animal Models Core, and on brain tissue from humans with substance use disorders (SUDs), and thereby provides a foundation for the more targeted measures in the individual Projects. Indeed, each Project focuses on genes that are among the most robustly regulated across rodent addiction models and human SUDs. As well, the Core pilots novel experimental technologies; an example is locus- specific epigenome editing to target single chromatin modifications to a single gene within a single brain region and cell type in vivo, thus providing an unparalleled level of proof to establish transcriptional mechanisms of addiction. By consolidating the analytical work and routine genome-wide analyses within a centralized Core, we ensure rigorous control over the data and facilitate comparisons of experimental findings across the four individual Projects. This consolidation also makes financial sense, as it maximize efficient use of our expertise. Finally, the Core is responsible, with the Administrative Core, for sharing our genome-wide datasets and analytical tools across the PPG’s laboratories as well as with the scientific community and lay public at large.