Figure 3. Accessible chromatin elements furnish cell subclass-specific AAV genetic tools.

(A) AAV2/PHP.eB viral reporter vector design for testing presumptive enhancers cloned upstream of a minimal promoter and SYFP2 reporter expression cassette in mouse retro-orbital assay.

(B) Transgene expression from AAV-hSyn1-H2B-SYFP2 in most neurons throughout mouse brain.

(C) Transgene expression from AAV-hDLXI56i-minBG-SYFP2 in mouse forebrain interneurons, in agreement with previous reports (Zerucha et al., 2000; Dimidschstein et al., 2016).

(D) Several identified enhancers showing ATAC-seq peaks in distinct target cell subclasses. Each selected enhancer is highlighted in yellow on read pileups, and heatmap below demonstrates ATAC-seq read CPM in all cell subclasses.

(E) Distinct expression patterns from these enhancer-AAV vectors in live 300-μm-thick slices of primary visual cortex (VISp) after retro-orbital delivery, consistent with different subclass-specific expression patterns.

(F) Multiplexed FISH in VISp region revealing differing subclass specificities from various enhancer-AAV vectors. Text represents mean ± SD for labeling specificity across three independent mice.

(G)scRNA-seq on sorted individual SYFP2⁺ cells from VISp region confirming distinct cell subclass transcriptomic identities labeled by the highlighted enhancer-AAV vectors.