Protein-guided RNA barcoding links transcriptomes to synaptic architecture

Mammalian brain function relies on the precise synaptic architecture of diverse cell types, yet scalable methods for linking a neuron's transcriptomic profile to its neuroanatomy remain limited. We present Synapse-seq, an in vivo strategy in which cell-identifying barcoded mRNAs are routed to subcellular compartments via targeting proteins and detected by single-cell and spatial genomics. Using AAV delivery for minimal perturbation of gene expression, we directed barcodes to presynaptic terminals (via synaptophysin) in four distinct circuits, or to postsynaptic sites (via nanobodies to endogenous PSD95) of hippocampal excitatory neurons. In the mouse primary visual cortex, presynaptic Synapse-seq recovered known long-range projections and discovered cortical layer subtypes with distinct thalamic innervation. In the anterior cortex, we elucidated simple topographic rules of corticostriatal innervation: intratelencephalic neurons followed a continuous depth-to-target gradient, while extratelencephalic neurons exhibited striatal collaterals that spatially correlated with medullary innervation. Finally, postsynaptic barcoding of excitatory neurons revealed cell type-specific variation in dendritic architectures across and within hippocampal subfields. These data establish Synapse-seq as a versatile, genomics-based approach for the integrated definition of molecular identity and synaptic organization across mammalian brains.