Abstract
Enhancers are the primary DNA regulatory elements that confer cell type specificity of gene expression. Recent studies characterizing individual enhancers have revealed their potential to direct heterologous gene expression in a highly cell-type-specific manner. However, it has not yet been possible to systematically identify and test the function of enhancers for each of the many cell types in an organism. We have developed PESCA, a scalable and generalizable method that leverages ATAC- and single-cell RNA-sequencing protocols, to characterize cell-type-specific enhancers that should enable genetic access and perturbation of gene function across mammalian cell types. Focusing on the highly heterogeneous mammalian cerebral cortex, we apply PESCA to find enhancers and generate viral reagents capable of accessing and manipulating a subset of somatostatin-expressing cortical interneurons with high specificity. This study demonstrates the utility of this platform for developing new cell-type-specific viral reagents, with significant implications for both basic and translational research.
Highlights
Enhancers are DNA elements that regulate gene expression to produce the unique complement of proteins necessary to establish a specialized function for each cell type in an organism
To identify candidate SST interneuron-restricted gene regulatory elements (GREs), we carried out comparative epigenetic profiling of the three largest classes of cortical interneurons: somatostatin (SST), vasoactive intestinal polypeptide (VIP)- and parvalbumin (PV)-expressing cells
The assay for transposase-accessible chromatin using sequencing (ATAC-Seq) (Buenrostro et al, 2015), which identifies nucleosome-depleted gene regulatory regions, was used to identify genomic regions with enhanced accessibility in the SST (n = 57,932), PV (n = 61,108), and VIP (n = 79,124) chromatin samples (Figure 1b,c, Figure 1—figure supplement 1, Materials and methods). These datasets can be used as a resource to identify putative gene regulatory elements as candidates for driving cell-type-specific gene expression for the numerous subtypes of SST, PV or VIP-expressing intraneurons across diverse cortical regions
Summary
Enhancers are DNA elements that regulate gene expression to produce the unique complement of proteins necessary to establish a specialized function for each cell type in an organism. Characterization of individual enhancers has revealed their potential to direct highly cell-type-specific gene expression in both endogenous and heterologous contexts (Dimidschstein et al, 2016; Graybuck et al, 2019; Juttner et al, 2019; Mich et al, 2019), making them ideal for developing tools to access, study, and manipulate virtually any mammalian cell type.
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