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Alcohol exposure during the formation of the neural tube (gestational day [GD] 8 to 10 in mice; equivalent to4th week of human pregnancy) disrupts development of ventral midline brain structures such as the pituitary, septum, and ventricles. This study identifies transcriptomic changes in the rostroventral neural tube (RVNT), the region of the neural tube that gives rise to the midline structures sensitive to alcohol exposure during neurulation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Female C57BL\/6J mice were administered 2 doses of alcohol (2.9\u00a0g\/kg) or vehicle 4\u00a0hours apart on GD 9.0. The RVNTs of embryos were collected 6 or 24\u00a0hours after the first dose and processed for RNA\u2010seq.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Six hours following GD 9.0 alcohol exposure (GD 9.25), over 2,300 genes in the RVNT were determined to be differentially regulated by alcohol. Enrichment analysis determined that PAE affected pathways related to cell proliferation, p53 signaling, ribosome biogenesis, and immune activation. In addition, over 100 genes involved in primary cilia formation and function and regulation of morphogenic pathways were altered 6\u00a0hours after alcohol exposure. The changes to gene expression were largely transient, as only 91 genes identified as differentially regulated by prenatal alcohol at GD 10 (24\u00a0hours postexposure). Functionally, the differentially regulated genes at GD 10 were related to organogenesis and cell migration.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>These data give a comprehensive view of the changing landscape of the embryonic transcriptome networks in regions of the neural tube that give rise to brain structures impacted by a neurulation\u2010stage alcohol exposure. Identification of gene networks dysregulated by alcohol will help elucidate the pathogenic mechanisms of alcohol\u2019s actions.<\/jats:p><\/jats:sec>","DOI":"10.1111\/acer.14389","type":"journal-article","created":{"date-parts":[[2020,6,18]],"date-time":"2020-06-18T15:15:07Z","timestamp":1592493307000},"page":"1540-1550","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Transcriptome\u2010Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure"],"prefix":"10.1111","volume":"44","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5838-0016","authenticated-orcid":false,"given":"Karen E.","family":"Boschen","sequence":"first","affiliation":[{"name":"From the Bowles Center for Alcohol Studies The University of North Carolina at Chapel Hill Chapel Hill North Carolina USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Travis 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