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We report genes with intronic SVA transposons are enriched for neurodevelopmental disease and transcribed into long non-coding SVA-lncRNAs. Human-specific SVAs in microcephaly <jats:italic>CDK5RAP2<\/jats:italic> and epilepsy <jats:italic>SCN8A<\/jats:italic> gene introns repress their expression <jats:italic>via<\/jats:italic> transcription factor ZNF91 to delay neuronal maturation. Deleting the SVA in <jats:italic>CDK5RAP2<\/jats:italic> initiates multi-dimensional and in <jats:italic>SCN8A<\/jats:italic> selective sodium current neuronal maturation by upregulating these genes. SVA-lncRNA <jats:italic>AK057321<\/jats:italic> forms RNA:DNA heteroduplexes with the genomic SVAs and upregulates these genes to initiate neuronal maturation. SVA-lncRNA <jats:italic>AK057321<\/jats:italic> also promotes species-specific cortex and cerebellum-enriched expression upregulating human genes with intronic SVAs (e.g., <jats:italic>HTT<\/jats:italic>, <jats:italic>CHAF1B<\/jats:italic> and <jats:italic>KCNJ6<\/jats:italic>) but not mouse orthologs. The diversity of neuronal genes with intronic SVAs suggest this hominoid-specific SVA transposon-based gene regulatory mechanism may act at multiple steps to specialize and achieve neoteny of the human brain.<\/jats:p>","DOI":"10.1038\/s42003-023-04683-8","type":"journal-article","created":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T12:12:50Z","timestamp":1680178370000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Hominoid SVA-lncRNA AK057321 targets human-specific SVA retrotransposons in SCN8A and CDK5RAP2 to initiate neuronal maturation"],"prefix":"10.1038","volume":"6","author":[{"given":"Monica J. 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