{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T22:03:48Z","timestamp":1791929028907,"version":"4.3.4"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T00:00:00Z","timestamp":1702512000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T00:00:00Z","timestamp":1702512000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"The National Natural Science Fund","award":["82071690"],"award-info":[{"award-number":["82071690"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Epigenetics &amp; Chromatin"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Neural tube defects (NTDs) are one of the most severe congenital abnormalities characterized by failures of the neural tube to close during early embryogenesis. Maternal folate deficiency could impact the occurrence of NTDs, however, the mechanisms involved in the cause of NTDs are poorly defined.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here, we report that histone H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) expression was significantly downregulated, and low levels of H3K79me2 were found in the corresponding NTDs samples with their maternal serum folate under low levels. Using ChIP-seq assays, we found that a decrease of H3K79me2 downregulates the expression of <jats:italic>Shh<\/jats:italic> and <jats:italic>Sufu<\/jats:italic> in mouse embryonic stem cells (mESC) under folate deficiency. Interestingly, folate antagonist methotrexate treatment led to attenuation of H3K79me2 due to Dot1l, affecting <jats:italic>Shh<\/jats:italic> and <jats:italic>Sufu<\/jats:italic> genes regulation. Upon further analysis, we find that the genes Shh and Sufu are both downregulated in the brain tissues of mice and humans with NTDs. There was a positive correlation between the transcription levels of <jats:italic>Shh<\/jats:italic>, <jats:italic>Sufu<\/jats:italic> and the protein levels of DOT1L by Pearson correlation analysis.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Our results indicate that abnormal <jats:italic>Shh<\/jats:italic> and <jats:italic>Sufu<\/jats:italic> genes expression reduced by aberrant Dot1l-mediated H3K79me2 levels could be the cause of NTDs occurrence.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s13072-023-00517-3","type":"journal-article","created":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T04:22:52Z","timestamp":1702527772000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Folate deficiency reduced aberrant level of DOT1L-mediated histone H3K79 methylation causes disruptive SHH gene expression involved in neural tube defects"],"prefix":"10.1186","volume":"16","author":[{"given":"Xue","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei","family":"Pei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinying","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changyun","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,12,14]]},"reference":[{"key":"517_CR1","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1146\/annurev-neuro-062012-170354","volume":"37","author":"ND Greene","year":"2014","unstructured":"Greene ND, Copp AJ. Neural tube defects. Annu Rev Neurosci. 2014;37:221\u201342.","journal-title":"Annu Rev Neurosci"},{"key":"517_CR2","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1146\/annurev-genet-120213-092208","volume":"48","author":"J Wilde","year":"2014","unstructured":"Wilde J, Petersen JR, Niswander L. Genetic, epigenetic, and environmental contributions to neural tube closure. Annu Rev Genet. 2014;48:583\u2013611.","journal-title":"Annu Rev Genet"},{"key":"517_CR3","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1002\/ajmg.1320580406","volume":"58","author":"MJ Seller","year":"1995","unstructured":"Seller MJ. Sex, neural tube defects, and multisite closure of the human neural tube. Am J Med Genet. 1995;58:332\u20136.","journal-title":"Am J Med Genet"},{"key":"517_CR4","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1002\/ajmg.c.30057","volume":"135","author":"LE Mitchell","year":"2005","unstructured":"Mitchell LE. Epidemiology of neural tube defects. Am J Med Genet C Semin Med Genet. 2005;135:88\u201394.","journal-title":"Am J Med Genet C Semin Med Genet"},{"key":"517_CR5","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1056\/NEJMoa067103","volume":"357","author":"P De Wals","year":"2007","unstructured":"De Wals P. Reduction in neural-tube defects after folic acid fortification in Canada. N Engl J Med. 2007;357:135\u201342.","journal-title":"N Engl J Med"},{"key":"517_CR6","doi-asserted-by":"publisher","first-page":"3678","DOI":"10.1093\/hmg\/ddr289","volume":"20","author":"A Marean","year":"2011","unstructured":"Marean A, Graf A, Zhang Y, Niswander L. Folic acid supplementation can adversely affect murine neural tube closure and embryonic survival. Hum Mol Genet. 2011;20:3678\u201383.","journal-title":"Hum Mol Genet"},{"key":"517_CR7","doi-asserted-by":"publisher","first-page":"2402","DOI":"10.3945\/jn.109.113670","volume":"139","author":"PJ Stover","year":"2009","unstructured":"Stover PJ. One-carbon metabolism-genome interactions in folate-associated pathologies. J Nutr. 2009;139:2402\u20135.","journal-title":"J Nutr"},{"key":"517_CR8","doi-asserted-by":"publisher","first-page":"789","DOI":"10.3945\/ajcn.110.002766","volume":"93","author":"AE Beaudin","year":"2011","unstructured":"Beaudin AE, Abarinov EV, Noden DM, Perry CA, Chu S, Stabler SP, et al. Shmt1 and de novo thymidylate biosynthesis underlie folate-responsive neural tube defects in mice. Am J Clin Nutr. 2011;93:789\u201398.","journal-title":"Am J Clin Nutr"},{"key":"517_CR9","doi-asserted-by":"publisher","first-page":"2107","DOI":"10.1126\/science.280.5372.2107","volume":"280","author":"A Fleming","year":"1998","unstructured":"Fleming A, Copp AJ. Embryonic folate metabolism and mouse neural tube defects. Science. 1998;280:2107\u20139.","journal-title":"Science"},{"issue":"Pt 4","key":"517_CR10","first-page":"1043","volume":"130","author":"LP Dunlevy","year":"2007","unstructured":"Dunlevy LP, Chitty LS, Burren KA, Doudney K, Stojilkovic-Mikic T, Stanier P, et al. Abnormal folate metabolism in foetuses affected by neural tube defects. Brain. 2007;130(Pt 4):1043\u20139.","journal-title":"Brain"},{"key":"517_CR11","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1002\/path.2643","volume":"220","author":"AJ Copp","year":"2010","unstructured":"Copp AJ, Greene ND. Genetics and development of neural tube defects. J Pathol. 2010;220:217\u201330.","journal-title":"J Pathol"},{"key":"517_CR12","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1016\/0301-0082(90)90037-H","volume":"35","author":"AJ Copp","year":"1990","unstructured":"Copp AJ, Brook FA, Estibeiro JP, Shum AS, Cockroft DL. The embryonic development of mammalian neural tube defects. Prog Neurobiol. 1990;35:363\u2013403.","journal-title":"Prog Neurobiol"},{"key":"517_CR13","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1002\/ajmg.c.30057","volume":"135C","author":"LE Mitchell","year":"2005","unstructured":"Mitchell LE. Epidemiology of neural tube defects. Am J Med Genet C Semin Med Genet. 2005;135C:88\u201394.","journal-title":"Am J Med Genet C Semin Med Genet"},{"key":"517_CR14","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.1016\/S1097-2765(03)00477-5","volume":"12","author":"AH Peters","year":"2003","unstructured":"Peters AH, Kubicek S, Mechtler K, et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol Cell. 2003;12:1577\u201389.","journal-title":"Mol Cell"},{"key":"517_CR15","doi-asserted-by":"publisher","first-page":"2999","DOI":"10.1021\/bi100213t","volume":"49","author":"X Cheng","year":"2010","unstructured":"Cheng X, Blumenthal RM. Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochemistry. 2010;49:2999\u20133008.","journal-title":"Biochemistry"},{"key":"517_CR16","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.1093\/nar\/gkw1208","volume":"45","author":"Q Xie","year":"2017","unstructured":"Xie Q, Li C, Song X, Wu L, Jiang Q, Qiu Z, et al. Folate deficiency facilitates recruitment of upstream binding factor to hot spots of DNA double strand breaks of rRNA genes and promotes its transcription. Nucleic Acids Res. 2017;45:2472\u201389.","journal-title":"Nucleic Acids Res"},{"key":"517_CR17","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/j.nbd.2013.01.014","volume":"54","author":"Q Zhang","year":"2013","unstructured":"Zhang Q, Xue P, et al. Histone modification mapping in human brain reveals aberrant expression of histone H3 lysine 79 dimethylation in neural tube defects. Neurobiol Dis. 2013;54:404\u201313.","journal-title":"Neurobiol Dis"},{"key":"517_CR18","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/j.nbd.2013.01.014","volume":"54","author":"Q Zhang","year":"2013","unstructured":"Zhang Q, Xue P, Li H, et al. Histone modification mapping in human brain reveals aberrant expression of histone H3 lysine 79 dimethylation in neural tube defects. Neurobiol Dis. 2013;54:404\u201313.","journal-title":"Neurobiol Dis"},{"key":"517_CR19","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1016\/S0092-8674(02)00759-6","volume":"109","author":"F van Leeuwen","year":"2002","unstructured":"van Leeuwen F, Gafken PR, Gottschling DE. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell. 2002;109:745\u201356.","journal-title":"Cell"},{"key":"517_CR20","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1101\/gad.2057811","volume":"25","author":"AT Nguyen","year":"2001","unstructured":"Nguyen AT, Zhang. Y. The diverse functions of Dot1 and H3K79 methylation. Genes Dev. 2001;25:1345\u201358.","journal-title":"Genes Dev"},{"key":"517_CR21","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1007\/s10930-010-9242-8","volume":"29","author":"G Park","year":"2010","unstructured":"Park G, et al. Characterization of the DOT1L network implications of diverse. Protein J. 2010;29:213\u201323.","journal-title":"Protein J"},{"key":"517_CR22","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/cdd.2014.199","volume":"23","author":"P Cattaneo","year":"2016","unstructured":"Cattaneo P, Kunderfranco P, et al. DOT1L-mediated H3K79me2 modification critically regulates gene expression during cardiomyocyte differentiation. Cell Death Diff. 2016;23:555\u201364.","journal-title":"Cell Death Diff"},{"key":"517_CR23","doi-asserted-by":"publisher","first-page":"4273","DOI":"10.1007\/s12035-018-1377-1","volume":"56","author":"PP Bovio","year":"2019","unstructured":"Bovio PP, Franz H, Heidrich S, Rauleac T, Kilpert F, Manke T, et al. Differential methylation of H3K79 reveals DOT1L target genes and function in the cerebellum in vivo. Mol Neurobiol. 2019;56:4273\u201387.","journal-title":"Mol Neurobiol"},{"key":"517_CR24","doi-asserted-by":"publisher","first-page":"7042","DOI":"10.1073\/pnas.0912041107","volume":"107","author":"N B\u00fcttner","year":"2010","unstructured":"B\u00fcttner N, Johnsen SA, K\u00fcgler S, Vogel T. Af9\/Mllt3 interferes with Tbr1 expression through epigenetic modification of histone H3K79 during development of the cerebral cortex. Proc Natl Acad Sci U S A. 2010;107:7042\u20137.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"517_CR25","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1093\/nar\/gky953","volume":"47","author":"H Franz","year":"2019","unstructured":"Franz H, Villarreal A, Heidrich S, Videm P, Kilpert F, Mestres I, et al. DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex. Nucleic Acids Res. 2019;47:168\u201383.","journal-title":"Nucleic Acids Res"},{"key":"517_CR26","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1002\/stem.2187","volume":"34","author":"D Roidl","year":"2016","unstructured":"Roidl D, Hellbach N, Bovio PP, Villarreal A, Heidrich S, Nestel S, et al. DOT1L activity promotes proliferation and protects cortical neural stem cells from activation of ATF4-DDIT3-mediated ER stress in vitro. Stem Cells. 2016;34:233\u201345.","journal-title":"Stem Cells"},{"key":"517_CR27","doi-asserted-by":"publisher","first-page":"R113","DOI":"10.1093\/hmg\/ddp347","volume":"18","author":"ND Greene","year":"2009","unstructured":"Greene ND, Stanier P, Copp AJ. Genetics of human neural tube defects. Hum Mol Genet. 2009;18:R113\u201329.","journal-title":"Hum Mol Genet"},{"key":"517_CR28","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1016\/S1028-4559(08)60003-0","volume":"46","author":"CP Chen","year":"2007","unstructured":"Chen CP. Chromosomal abnormalities associated with neural tube defects (II): partial aneuploidy. Taiwan J Obstet Gynecol. 2007;46:336\u201351.","journal-title":"Taiwan J Obstet Gynecol"},{"key":"517_CR29","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1016\/S1028-4559(08)60002-9","volume":"46","author":"CP Chen","year":"2007","unstructured":"Chen CP. Chromosomal abnormalities associated with neural tube defects (I): full aneuploidy. Taiwan J Obstet Gynecol. 2007;46:325\u201335.","journal-title":"Taiwan J Obstet Gynecol"},{"key":"517_CR30","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/nn983","volume":"6","author":"K Lai","year":"2009","unstructured":"Lai K, Kaspar BK, Gage FH, Schaffer DV. Sonic hedgehog regulates adult neural progenitor proliferation in vitro and in vivo. Nat Neurosci. 2009;6:21\u20137.","journal-title":"Nat Neurosci"},{"key":"517_CR31","doi-asserted-by":"publisher","first-page":"1683","DOI":"10.1093\/hmg\/8.9.1683","volume":"81","author":"S Odent","year":"1999","unstructured":"Odent S, Atti-Bitach T, et al. Expression of the Sonic hedgehog (SHH)gene during early human development and phenotypic expression of new mutations causing holoprosencephaly. Hum Mol Genet. 1999;81:1683\u20139.","journal-title":"Hum Mol Genet"},{"key":"517_CR32","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1038\/383407a0","volume":"383","author":"C Chiang","year":"1996","unstructured":"Chiang C, Litingtung Y, Lee E, et al. Cyclopia and defective axial patterning in mice lacking Sonic hedgehog gene function. Nature. 1996;383:407\u201313.","journal-title":"Nature"},{"key":"517_CR33","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/j.devcel.2005.12.013","volume":"10","author":"J Svard","year":"2006","unstructured":"Svard J, Heby-Henricson K, Persson-Lek M, et al. Genetic elimination of Suppressor of fused reveals an essential repressor function in the mammalian Hedgehog signalling pathway. Dev Cell. 2006;10:187\u201397.","journal-title":"Dev Cell"},{"key":"517_CR34","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/S0925-4773(98)00139-7","volume":"77","author":"E Stanley","year":"1998","unstructured":"Stanley E, Biben C, et al. DAN is a secreted glycoprotein related to Xenopus cerberus. Mech Dev. 1998;77:173\u201384.","journal-title":"Mech Dev"},{"key":"517_CR35","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.mrgentox.2008.11.011","volume":"673","author":"S Padmanabhan","year":"2009","unstructured":"Padmanabhan S, Tripathi DN, et al. Methotrexate-induced cytotoxicity and genotoxicity in germ cells of mice: intervention of folic and folinic acid. Mut Res. 2009;673:43\u201352.","journal-title":"Mut Res."},{"key":"517_CR36","doi-asserted-by":"publisher","DOI":"10.1186\/s13072-019-0312-7","author":"P Pei","year":"2019","unstructured":"Pei P, Cheng X, et al. Folate deficiency induced H2A ubiquitination to lead to downregulated expression of genes involved in neural tube defects. Epigenetics Chromatin. 2019. https:\/\/doi.org\/10.1186\/s13072-019-0312-7.","journal-title":"Epigenetics Chromatin"},{"key":"517_CR37","doi-asserted-by":"publisher","first-page":"1455","DOI":"10.1002\/bdr2.1380","volume":"111","author":"L Avagliano","year":"2019","unstructured":"Avagliano L, Massa V, et al. Overview on Neural tube defects: from development to physical characteristics. Birth Defects Res. 2019;111:1455\u201367.","journal-title":"Birth Defects Res"},{"key":"517_CR38","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/0140-6736(91)90133-A","volume":"338","author":"MRC Vitamin Study Research Group","year":"1991","unstructured":"MRC Vitamin Study Research Group. Prevention of neural tube defects: results of the Medical Research Council Vitamin Study. Lancet. 1991;338:131\u20137.","journal-title":"Lancet"},{"key":"517_CR39","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1002\/bdrc.20100","volume":"81","author":"AE Beaudin","year":"2007","unstructured":"Beaudin AE, Stover PJ. Folate-mediated one-carbon metabolism and neural tube defects: balancing genome synthesis and gene expression. Birth Defects Res C Embryo Today. 2007;81:183\u2013203.","journal-title":"Birth Defects Res C Embryo Today"},{"key":"517_CR40","doi-asserted-by":"publisher","first-page":"36922","DOI":"10.1074\/jbc.M110.126714","volume":"285","author":"S Ichi","year":"2010","unstructured":"Ichi S, Costa FF, Bischof JM, et al. Folic acid remodels chromatin on Hes1 and Neurog2 promoters during caudal neural tube development. J Biol Chem. 2010;285:36922\u201332.","journal-title":"J Biol Chem"},{"key":"517_CR41","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1242\/dev.101550","volume":"141","author":"T Zhao","year":"2014","unstructured":"Zhao T, Gan Q, Stokes A, et al. beta-catenin regulates Pax3 and Cdx2 for caudal neural tube closure and elongation. Development. 2014;141:148\u201357.","journal-title":"Development"},{"key":"517_CR42","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1101\/gad.2057811","volume":"25","author":"AT Nguyen","year":"2011","unstructured":"Nguyen AT, Zhang Y. The diverse functions of Dot1 and H3K79 methylation. Genes Dev. 2011;25:1345\u201358.","journal-title":"Genes Dev"}],"container-title":["Epigenetics &amp; Chromatin"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13072-023-00517-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13072-023-00517-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13072-023-00517-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T05:04:06Z","timestamp":1702530246000},"score":1,"resource":{"primary":{"URL":"https:\/\/epigeneticsandchromatin.biomedcentral.com\/articles\/10.1186\/s13072-023-00517-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,14]]},"references-count":42,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["517"],"URL":"https:\/\/doi.org\/10.1186\/s13072-023-00517-3","relation":{},"ISSN":["1756-8935"],"issn-type":[{"value":"1756-8935","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,14]]},"assertion":[{"value":"2 August 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 October 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 December 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Both animal and human samples used in this study are approved by the Ethics Board of Capital Institute of Pediatrics with Ethics Review Number DWLL2021011 and SHERLLM2021024. The human samples were secondary utilization of the previous samples with exception to the requirement of informed consent. We have attached the Ethical approval of the previous study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"50"}}