Assessing the Nanoscale Organization of Excitatory and Inhibitory Synapses Using Recombinant Probes to Visualize Endogenous Synaptic Proteins

Synapses are highly dynamic and complex structures responsible for neuronal communication. The recent progresses in super-resolution imaging technologies unraveled an inherently complex nanorganization ofsynaptic components. At the single synapse level, nanodomains of key proteins of pre- and postsynaptic terminals are transcellularly aligned in nanocolumns, which turned out to have a significant impact onsynaptic function. Perturbations of this dynamic organization might also be involved in neurodevelopmental disorders, such as autism and intellectual disability. Therefore, it is crucial to understand theorganization principles of synaptic connections and their dynamic regulation with nanometer precision. Here, we present a detailed protocol that enables to visualize endogenous synaptic proteins both in vitroand in vivo. This method combines the use of transcriptionally regulated fibronectin intrabodies generated with mRNA display (FingRs) against PSD95 and Gephyrin, two major scaffolding proteins of excitatoryand inhibitory synapses, with in utero electroporation (IUE), confocal, and stimulated emission depletion (STED) microscopy. This approach may be considered as a method of choice to assess a number ofmorphometric parameters of synaptic connections up to their nanoscale organization. We believe that this strategy might help to progress our understanding of the molecular mechanisms underlying brainfunction and dysfunction.