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A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However  systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep  also called lnc rps25  and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein  Hmgn1  and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically  we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes   evolutionarily newer cell types that develop postnatally in humans. 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