Viral genetic tools to target specific brain cell types in humans and nongenetic model organisms will transform basic neuroscience and targeted gene therapy. Here we used comparative epigenetics to identify thousands of human neuronal subclass-specific putative enhancers to regulate viral tools, and 34% of these were conserved in mouse. We established an AAV platform to evaluate cellular specificity of functional enhancers by multiplexed fluorescent in situ hybridization (FISH) and single cell RNA sequencing. Initial testing in mouse neocortex yields a functional enhancer discovery success rate of over 30%. We identify enhancers with specificity for excitatory and inhibitory classes and subclasses including PVALB, LAMP5, and VIP/LAMP5 cells, some of which maintain specificity in vivo or ex vivo in monkey and human neocortex. Finally, functional enhancers can be proximal or distal to cellular marker genes, conserved or divergent across species, and could yield brain-wide specificity greater than the most selective marker genes.
Keywords: Human, macaque, brain cell types, epigenetics, enhancers, AAVs, neocortex, reporters, genetic tools, ex vivo brain slice, ATAC-seq, RNA-seq, Parvalbumin
Mich, John K. and Graybuck, Lucas T. and Hess, Erik and Mahoney, Joseph and Kojima, Yoshiko and Ding, Yi and Somasundaram, Saroja and Miller, Jeremy A. and Weed, Natalie and Omstead, Victoria and Bishaw, Yemeserach and Shapovalova, Nadiya and Martinez, Refugio and Fong, Olivia and Yao, Shenqin and Mortrud, Marty and Chong, Peter and Loftus, Luke and Bertagnolli, Darren and Goldy, Jeff and Casper, Tamara and Dee, Nick and Opitz-Araya, Ximena and Cetin, Ali and Smith, Kimberly A. and Gwinn, Ryder P. and Cobbs, Charles and Ko, Andrew L. and Ojemann, Jeffrey G. and Keene, C. Dirk and Silbergeld, Daniel L. and Sunkin, Susan M. and Gradinaru, Viviana and Horwitz, Gregory D. and Zeng, Hongkui and Tasic, Bosiljka and Lein, Ed and Ting, Jonathan and Levi, Boaz, Functional Enhancer Elements Drive Subclass-Selective Expression from Mouse to Primate Neocortex. Available at SSRN: https://ssrn.com/abstract=3584741 or http://dx.doi.org/10.2139/ssrn.3584741
This version of the paper has not been formally peer reviewed.
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