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Herein, we searched for genes with hypermethylated promoter region and downregulated transcript level to reveal irreversible markers of developmental neurotoxicity. The hippocampal dentate gyrus of male rat offspring exposed maternally to PTU, VPA, or GLY was subjected to Methyl\u2010Seq and RNA\u2010Seq analyses on postnatal day (PND) 21. Among the genes identified, 170 were selected for further validation analysis of gene expression on PND 21 and PND 77 by real\u2010time reverse transcription\u2010PCR. PTU and GLY downregulated many genes on PND 21, reflecting diverse effects on neurogenesis. Furthermore, genes showing sustained downregulation were found after PTU or VPA exposure, reflecting a sustained or late effect on neurogenesis by these compounds. In contrast, such genes were not observed with GLY, probably because of the reversible nature of the effects. Among the genes showing sustained downregulation, <jats:italic>Creb<\/jats:italic>, <jats:italic>Arc<\/jats:italic>, and <jats:italic>Hes5<\/jats:italic> were concurrently downregulated by PTU, suggesting an association with neuronal mismigration, suppressed synaptic plasticity, and reduction in neural stem and progenitor cells. <jats:italic>Epha7<\/jats:italic> and <jats:italic>Pvalb<\/jats:italic> were also concurrently downregulated by PTU, suggesting an association with the reduction in late\u2010stage progenitor cells. VPA induced sustained downregulation of <jats:italic>Vgf<\/jats:italic> and <jats:italic>Dpysl4<\/jats:italic>, which may be related to the aberrations in synaptic plasticity. The genes showing sustained downregulation may be irreversible markers of developmental neurotoxicity.<\/jats:p>","DOI":"10.1002\/jat.4089","type":"journal-article","created":{"date-parts":[[2020,11,4]],"date-time":"2020-11-04T20:59:50Z","timestamp":1604523590000},"page":"1021-1037","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Identification of gene targets of developmental neurotoxicity focusing on DNA hypermethylation involved in irreversible disruption of hippocampal neurogenesis in rats"],"prefix":"10.1002","volume":"41","author":[{"given":"Satomi","family":"Kikuchi","sequence":"first","affiliation":[{"name":"Laboratory of Veterinary Pathology, Division of Animal Life Science, Institute of Agriculture Tokyo University of Agriculture and Technology  Tokyo Japan"},{"name":"Cooperative Division of Veterinary Sciences, Graduate School of Agriculture Tokyo University of Agriculture and Technology  Tokyo 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