{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T19:40:44Z","timestamp":1790278844770,"version":"4.1.0"},"reference-count":52,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T00:00:00Z","timestamp":1666396800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Research Council of Thailand","award":["RGNS 64\u2013056"],"award-info":[{"award-number":["RGNS 64\u2013056"]}]},{"name":"National Science and Technology Development Agency Thailand","award":["RGNS 64\u2013056"],"award-info":[{"award-number":["RGNS 64\u2013056"]}]},{"name":"Chiang Mai University Center of Excellence Award","award":["RGNS 64\u2013056"],"award-info":[{"award-number":["RGNS 64\u2013056"]}]},{"name":"Office of the Permanent Secretary, Ministry of Higher Education, Science, Research, and Innovation","award":["RGNS 64\u2013056"],"award-info":[{"award-number":["RGNS 64\u2013056"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Orofacial clefts are among the most common craniofacial anomalies with multifactorial etiologies, including genetics and environments. DNA methylation, one of the most acknowledged mechanisms of epigenetics, is involved in the development of orofacial clefts. DNA methylation has been examined in patients with non-syndromic cleft lip with cleft palate (nsCL\/P) from multiple specimens, including blood, saliva, lip, and palate, as well as experimental studies in mice. The results can be reported in two different trends: hypomethylation and hypermethylation. Both hypomethylation and hypermethylation can potentially increase the risk of nsCL\/P depending on the types of specimens and the specific regions on each gene and chromosome. This is the most up-to-date review, intending to summarize evidence of the alterations of DNA methylation in association with the occurrence of orofacial clefts. To make things straightforward to understand, we have systematically categorized the data into four main groups: human blood, human tissues, animal models, and the factors associated with DNA methylation. With this review, we are moving closer to the core of DNA methylation associated with nsCL\/P development; we hope this is the initial step to find a genetic tool for early detection and prevention of the occurrence of nsCL\/P.<\/jats:p>","DOI":"10.3390\/ijms232112727","type":"journal-article","created":{"date-parts":[[2022,10,24]],"date-time":"2022-10-24T04:40:36Z","timestamp":1666586436000},"page":"12727","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Alterations in DNA Methylation in Orofacial Clefts"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1731-6653","authenticated-orcid":false,"given":"Chirakan","family":"Charoenvicha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wimon","family":"Sirimaharaj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krit","family":"Khwanngern","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nipon","family":"Chattipakorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1677-7052","authenticated-orcid":false,"given":"Siriporn","family":"Chattipakorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"R73","DOI":"10.1093\/hmg\/ddh052","article-title":"Genetics of cleft lip and palate: Syndromic genes contribute to the incidence of non-syndromic clefts","volume":"13","author":"Stanier","year":"2004","journal-title":"Hum. Mol. Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1159\/000337464","article-title":"Epidemiology of oral clefts 2012: An international perspective","volume":"16","author":"Mossey","year":"2012","journal-title":"Front. Oral. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/nrg2933","article-title":"Cleft lip and palate: Understanding genetic and environmental influences","volume":"12","author":"Dixon","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"ref_4","first-page":"21","article-title":"Mutation analysis of the MSX1 gene exons and intron in patients with nonsyndromic cleft lip and palate","volume":"8","author":"Lace","year":"2006","journal-title":"Stomatologija"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"64","DOI":"10.4103\/0973-029X.92976","article-title":"A comprehensive review of the genetic basis of cleft lip and palate","volume":"16","author":"Kohli","year":"2012","journal-title":"J. Oral Maxillofac. Pathol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1097\/00008480-200112000-00011","article-title":"The genetics and epigenetics of orofacial clefts","volume":"13","author":"Spritz","year":"2001","journal-title":"Curr. Opin. Pediatr."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1016\/S0140-6736(09)60695-4","article-title":"Cleft lip and palate","volume":"374","author":"Mossey","year":"2009","journal-title":"Lancet"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1002\/bdr2.1802","article-title":"Role of epigenetics and miRNAs in orofacial clefts","volume":"112","author":"Garland","year":"2020","journal-title":"Birth Defects Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/nsmb.2489","article-title":"Epigenetic programming and reprogramming during development","volume":"20","author":"Cantone","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1597\/16-124","article-title":"Epigenetics and Orofacial Clefts: A Brief Introduction","volume":"55","author":"Sharp","year":"2018","journal-title":"Cleft Palate Craniofac. J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1002\/bdr2.1564","article-title":"Nucleic acid methylation and orofacial morphogenesis","volume":"111","author":"Seelan","year":"2019","journal-title":"Birth Defects Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3195","DOI":"10.1242\/dev.122.10.3195","article-title":"De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells","volume":"122","author":"Lei","year":"1996","journal-title":"Development"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nrg3230","article-title":"Functions of DNA methylation: Islands, start sites, gene bodies and beyond","volume":"13","author":"Jones","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1002\/bdrc.20180","article-title":"Palate morphogenesis: Current understanding and future directions","volume":"90","author":"Greene","year":"2010","journal-title":"Birth Defects Res. Part C Embryo Today Rev."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1002\/tera.1420500504","article-title":"Cell death and cell cycle perturbation in the developmental toxicity of the demethylating agent, 5-aza-2\u2019-deoxycytidine","volume":"50","author":"Rogers","year":"1994","journal-title":"Teratology"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1016\/j.ajhg.2016.02.019","article-title":"DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis","volume":"98","author":"Joubert","year":"2016","journal-title":"Am. J. Hum. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1093\/ije\/dyv042","article-title":"Maternal pre-pregnancy BMI and gestational weight gain, offspring DNA methylation and later offspring adiposity: Findings from the Avon Longitudinal Study of Parents and Children","volume":"44","author":"Sharp","year":"2015","journal-title":"Int. J. Epidemiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2441","DOI":"10.1038\/s41598-017-02721-0","article-title":"Differential methylation is associated with non-syndromic cleft lip and palate and contributes to penetrance effects","volume":"7","author":"Alvizi","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"133","DOI":"10.2217\/epi-2018-0091","article-title":"Evidence for DNA methylation mediating genetic liability to non-syndromic cleft lip\/palate","volume":"11","author":"Howe","year":"2019","journal-title":"Epigenomics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13148-019-0638-9","article-title":"A comparison of DNA methylation in newborn blood samples from infants with and without orofacial clefts","volume":"11","author":"Xu","year":"2019","journal-title":"Clin. Epigenetics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1111\/odi.12965","article-title":"Association of long interspersed nucleotide element-1 and interferon regulatory factor 6 methylation changes with nonsyndromic cleft lip with or without cleft palate","volume":"25","author":"Li","year":"2019","journal-title":"Oral Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1423-0127-21-7","article-title":"CITED2 mutation and methylation in children with congenital heart disease","volume":"21","author":"Xu","year":"2014","journal-title":"J. Biomed. Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1002\/bdra.20670","article-title":"Global DNA hypomethylation is associated with NTD-affected pregnancy: A case-control study","volume":"88","author":"Chen","year":"2010","journal-title":"Birth Defects Res. Part A Clin. Mol. Teratol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.3945\/ajcn.2009.28858","article-title":"Relation between hypomethylation of long interspersed nucleotide elements and risk of neural tube defects","volume":"91","author":"Wang","year":"2010","journal-title":"Am. J. Clin. Nutr."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/s13148-017-0362-2","article-title":"Distinct DNA methylation profiles in subtypes of orofacial cleft","volume":"9","author":"Sharp","year":"2017","journal-title":"Clin. Epigenetics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"105","DOI":"10.2217\/epi-2017-0081","article-title":"Evaluating LINE-1 methylation in cleft lip tissues and its association with early pregnancy exposures","volume":"10","author":"Khan","year":"2018","journal-title":"Epigenomics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1111\/odi.13136","article-title":"LINE-1 methylation in cleft lip tissues: Influence of infant MTHFR c.677C>T genotype","volume":"25","author":"Khan","year":"2019","journal-title":"Oral Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1002\/(SICI)1096-8628(19990903)86:1<71::AID-AJMG14>3.0.CO;2-Y","article-title":"Methylenetetrahydrofolate reductase thermolabile variant and oral clefts","volume":"86","author":"Mills","year":"1999","journal-title":"Am. J. Med. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1136\/jmg.39.5.368","article-title":"Maternal MTHFR genotype contributes to the risk of non-syndromic cleft lip and palate","volume":"39","author":"Prescott","year":"2002","journal-title":"J. Med. Genet."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1159\/000329935","article-title":"Urinary tract anomalies associated with MTHFR gene polymorphism C677T in girls","volume":"34","author":"Behunova","year":"2011","journal-title":"Kidney Blood Press. Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1002\/ajmg.10496","article-title":"MTHFR is not a risk factor in the development of isolated nonsyndromic cleft lip and palate","volume":"110","author":"Blanton","year":"2002","journal-title":"Am. J. Med. Genet."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3752","DOI":"10.1093\/hmg\/ddv119","article-title":"Longitudinal analysis of DNA methylation associated with birth weight and gestational age","volume":"24","author":"Simpkin","year":"2015","journal-title":"Hum. Mol. Genet."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s13148-015-0064-6","article-title":"Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes","volume":"7","author":"Acevedo","year":"2015","journal-title":"Clin. Epigenetics"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"656865","DOI":"10.3389\/fcell.2021.656865","article-title":"DNA Methylation Variation Is Identified in Monozygotic Twins Discordant for Non-syndromic Cleft Lip and Palate","volume":"9","author":"Young","year":"2021","journal-title":"Front. Cell. Dev. Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1002\/ajmg.b.32278","article-title":"DNA extracted from saliva for methylation studies of psychiatric traits: Evidence tissue specificity and relatedness to brain","volume":"168","author":"Smith","year":"2015","journal-title":"Am. J. Med. Genet. Part B Neuropsychiatr. Genet."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.semcdb.2013.12.001","article-title":"Salivary gland development: A template for regeneration","volume":"25-26","author":"Patel","year":"2014","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.1002\/dvdy.110","article-title":"Nonlinear gene expression-phenotype relationships contribute to variation and clefting in the A\/WySn mouse","volume":"248","author":"Green","year":"2019","journal-title":"Dev. Dyn."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e20180649","DOI":"10.1590\/1678-7757-2018-0649","article-title":"DNA hypermethylation of Fgf16 and Tbx22 associated with cleft palate during palatal fusion","volume":"27","author":"Shu","year":"2019","journal-title":"J. Appl. Oral Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1002\/bdra.20430","article-title":"Mouse genetic models of cleft lip with or without cleft palate","volume":"82","author":"Juriloff","year":"2008","journal-title":"Birth Defects Res. Part A Clin. Mol. Teratol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1002\/bdra.20106","article-title":"Investigations of the genomic region that contains the clf1 mutation, a causal gene in multifactorial cleft lip and palate in mice","volume":"73","author":"Juriloff","year":"2005","journal-title":"Birth Defects Res. Part A Clin. Mol. Teratol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1002\/bdra.20788","article-title":"The clf2 gene has an epigenetic role in the multifactorial etiology of cleft lip and palate in the A\/WySn mouse strain","volume":"91","author":"Plamondon","year":"2011","journal-title":"Birth Defects Res. Part A Clin. Mol. Teratol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1002\/bdra.23320","article-title":"Epigenetic mechanism causes Wnt9b deficiency and nonsyndromic cleft lip and palate in the A\/WySn mouse strain","volume":"100","author":"Juriloff","year":"2014","journal-title":"Birth Defects Res. Part A Clin. Mol. Teratol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.reprotox.2015.10.009","article-title":"Cigarette smoke induces proteasomal-mediated degradation of DNA methyltransferases and methyl CpG-\/CpG domain-binding proteins in embryonic orofacial cells","volume":"58","author":"Mukhopadhyay","year":"2015","journal-title":"Reprod. Toxicol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1016\/j.bbrc.2015.01.148","article-title":"Retinoic acid inhibits histone methyltransferase Whsc1 during palatogenesis","volume":"458","author":"Liu","year":"2015","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1597\/07-134.1","article-title":"DNA methylation changes during cleft palate formation induced by retinoic acid in mice","volume":"45","author":"Kuriyama","year":"2008","journal-title":"Cleft Palate Craniofac. J."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1089\/dna.2018.4369","article-title":"Genome-Wide DNA Methylation Profile of Gene cis-Acting Element Methylations in All-trans Retinoic Acid-Induced Mouse Cleft Palate","volume":"37","author":"Shu","year":"2018","journal-title":"DNA Cell Biol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1097\/SCS.0b013e3181ec6992","article-title":"Genes, environment, and orofacial clefting: N-acetyltransferase and folic acid","volume":"21","author":"Erickson","year":"2010","journal-title":"J. Craniofac. Surg."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1007\/s43032-020-00161-2","article-title":"Maternal Folic Acid Supplementation Mediates Offspring Health via DNA Methylation","volume":"27","author":"Liu","year":"2020","journal-title":"Reprod. Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1093\/ije\/dyy032","article-title":"The long-term impact of folic acid in pregnancy on offspring DNA methylation: Follow-up of the Aberdeen Folic Acid Supplementation Trial (AFAST)","volume":"47","author":"Richmond","year":"2018","journal-title":"Int. J. Epidemiol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1038\/s41390-018-0267-6","article-title":"Maternal folic acid supplementation reduces the severity of cleft palate in Tgf-\u03b2(3) null mutant mice","volume":"85","author":"Maldonado","year":"2019","journal-title":"Pediatr. Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1080\/15592294.2019.1581591","article-title":"Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk","volume":"14","author":"Gonseth","year":"2019","journal-title":"Epigenetics"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1002\/bdra.20488","article-title":"Genome-wide pathway analysis of folate-responsive genes to unravel the pathogenesis of orofacial clefting in man","volume":"82","author":"Bliek","year":"2008","journal-title":"Birth Defects Res. Part A Clin. Mol. Teratol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/21\/12727\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:00:54Z","timestamp":1760144454000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/21\/12727"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,22]]},"references-count":52,"journal-issue":{"issue":"21","published-online":{"date-parts":[[2022,11]]}},"alternative-id":["ijms232112727"],"URL":"https:\/\/doi.org\/10.3390\/ijms232112727","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,10,22]]}}}