Protein-guided RNA barcoding links transcriptomes to synaptic architecture

Area of Science:

• Neuroscience
• Genomics
• Molecular Biology

Background:

• Mammalian brain function depends on intricate synaptic connections between diverse cell types.
• Existing methods struggle to link neuronal transcriptomic data with precise neuroanatomical information.
• Scalable techniques are needed to map neuronal connectivity and molecular identity simultaneously.

Purpose of the Study:

• To develop and validate Synapse-seq, a novel in vivo strategy for linking transcriptomic profiles with synaptic organization.
• To investigate the neuroanatomical organization of specific brain circuits in the mouse.
• To explore cell type-specific variations in dendritic architecture.

Main Methods:

• Synapse-seq utilizes adeno-associated virus (AAV) delivery to route cell-identifying barcoded messenger RNAs (mRNAs) to subcellular compartments.
• Barcodes are targeted to presynaptic terminals using synaptophysin or to postsynaptic sites via nanobodies targeting PSD95.
• Single-cell and spatial genomics techniques are employed for barcode detection and analysis.

Main Results:

• Presynaptic Synapse-seq in the visual cortex identified known projections and novel cortical layer subtypes with specific thalamic innervation.
• Analysis of corticostriatal innervation revealed topographic rules for intratelencephalic and extratelencephalic neurons.
• Postsynaptic barcoding in the hippocampus demonstrated cell type-specific dendritic architecture variations.

Conclusions:

• Synapse-seq provides a versatile, genomics-based platform for integrated analysis of molecular identity and synaptic organization.
• The method enables high-resolution mapping of neuronal connectivity and circuit architecture.
• This approach advances our understanding of mammalian brain organization at the molecular and anatomical levels.