The small ORF (smORF)-encoded polypeptide MIRINE promotes neuronal differentiation in vertebrate brain development

The vertebrate brain expresses an extensive repertoire of long-noncoding RNAs (lncRNAs), an emerging source of small open reading frame (smORF)-encoded polypeptides (SEPs) whose functions remain largely unknown. Using ribosome profiling and proteomics of zebrafish and mouse brain, we identified hundreds of translated smORFs. We characterized MIRINE, a SEP of 83 amino acids conserved across 205 vertebrate species. MIRINE contains a transmembrane domain that targets it to the plasma membrane and intracellular vesicles, and is enriched in cortical and hippocampal neurons, with expression rising during neurogenesis. Downregulation of Mirine increased cell proliferation and impaired neuronal maturation in neuroblastoma cells, in mouse primary cortical neurons and cortex, and in the zebrafish forebrain, identifying MIRINE as a regulator of the balance between neuronal proliferation and differentiation. Mechanistically, MIRINE associates with the synaptic-vesicle protein Synaptogyrin-3 and related membrane proteins. Our findings define a conserved, membrane-associated SEP controlling neuronal maturation and illustrate the functional potential of brain SEPs.