A human-specific microRNA controls the timing of excitatory synaptogenesis (pLNA dataset)

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. We found that inhibition of a human-specific microRNA, miR-1229-3p, alters the trajectory of human neuronal maturation and enhances excitatory synaptic transmission. Transcriptome analysis following miR-1229 knockdown revealed a downregulation of mitochondrial DNA (mtDNA) encoded genes. We further show that miR-1229 regulates mitochondrial morphology, mtDNA abundance and matrix calcium concentration, and that stimulation of mitochondrial metabolism rescues decreased calcium buffering in miR-1229-3p depleted neurons. Accordingly, miR-1229 directly targets an entire network of genes involved in mitochondrial function and ER-associated protein homeostasis. 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. Overall design: To explore gene expression regulation of candidate microRNAs in human neurons, we differentiated hiPSC into human neurons following an optimized protocol ("igNeurons") for 21 days and inhibited those microRNAs (namely miR-181c-5p, miR-1229-3p and miR-3943) from day 9 on. RNA was extracted from 4 independent differentiations and sent for polyA-RNA sequencing. Neurons treated with a control inhibitor (pLNA-Ctrl) as well as untreated neurons ("Empty") were used as control.