Abstract Neural circuit development in the human cortex is considerably prolonged in comparison to non-human primates, a trait that contributes to the remarkable cognitive capacity of modern humans. Here, we explore the regulatory role of non-coding RNAs, which dramatically expanded during brain evolution, in synapse development of human-induced pluripotent stem-cell derived neurons. Inhibition of a human-specific microRNA, miR-1229-3p, results in accelerated formation of excitatory synapses and enhanced synaptic transmission. Mechanistically, miR-1229-3p controls mitochondrial homeostasis by targeting important regulators of mitochondrial autophagy and fission, such as Pink1. Stimulation of mitochondrial metabolism rescues decreased calcium buffering in miR-1229-3p depleted neurons. Our findings reveal an important function of human-specific miR-1229-3p in developmental timing of human synaptogenesis and generally implicate non-coding RNAs in the control of human connectivity and cognition. One-Sentence Summary A human-specific microRNA slows down the formation and maturation of neuronal synapses by reducing mitochondrial metabolism and renewal.

A human-specific microRNA controls the timing of excitatory synaptogenesis