Trans-synaptic interactions organize the multiple steps of synaptic development and are critical to generate fully functional neuronal circuits. While trans-synaptic interactions are primarily mediated by cell adhesion molecules (CAMs), some directly involve ionotropic glutamate receptors (iGluRs). Here, we review the expanding extracellular and trans-synaptic proteome of iGluRs. We discuss the role of these molecular networks in specifying the formation of excitatory and inhibitory circuits and in the input-specific recruitment of iGluRs at synapses in various cell types and brain regions. We also shed light on human-specific mutations affecting iGluR-mediated trans-synaptic interactions that may provide unique features to the human brain and contribute to its susceptibility to neurodevelopmental disorders. Together, these data support a view in which iGluR function goes far beyond fast excitatory synaptic transmission by shaping the wiring and the functional properties of neural circuits.
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