{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T19:54:17Z","timestamp":1775850857966,"version":"3.50.1"},"posted":{"date-parts":[[2026,4,8]]},"group-title":"Genetic and Genomic Medicine","reference-count":47,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:00:00Z","timestamp":1775606400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,4,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Introduction<\/jats:title>\n                  <jats:p>Nonsyndromic cleft lip with or without cleft palate (NSCL\/P) is a common congenital malformation with complex etiology involving both genetic and environmental factors. Epigenetic mechanisms may mediate environmental contributions, but separating genetic from environmental effects remains challenging.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We present an epigenome-wide association study with 32 monozygotic and 22 dizygotic twin pairs discordant for NSCL\/P on blood and saliva samples. Differential methylation analysis was conducted using linear models to identify CpG sites showing significant methylation differences between affected and unaffected twins followed by functional annotation and pathway enrichment analysis.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    The top-ranked finding is a differentially methylated region comprising two CpG sites at the\n                    <jats:italic>CYP26A1<\/jats:italic>\n                    locus, cg12110262 (P = 3.21x10\n                    <jats:sup>-7<\/jats:sup>\n                    ) and cg15055355 (P = 1.39x10\n                    <jats:sup>-3<\/jats:sup>\n                    ).\n                    <jats:italic>CYP26A1<\/jats:italic>\n                    is essential for retinoic acid catabolism and craniofacial patterning. The chromatin regulator\n                    <jats:italic>ANKRD11<\/jats:italic>\n                    , which causes KBG syndrome featuring cleft palate was the second best hit. Differentially methylated CpG sites showed significant enrichment in craniofacial enhancers and overlap with multiple GWAS-validated cleft genes including\n                    <jats:italic>VAX1, PVRL1, SMAD3<\/jats:italic>\n                    , and\n                    <jats:italic>PRDM16<\/jats:italic>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Our findings implicate retinoic acid signaling and chromatin regulation in NSCL\/P etiology and demonstrate the value of discordant twin designs for distinguishing environmental from genetic epigenetic contributions to complex malformations.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.04.07.26350251","type":"posted-content","created":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T15:20:14Z","timestamp":1775661614000},"source":"Crossref","is-referenced-by-count":0,"title":["Epigenetic Signatures in Monozygotic and Dizygotic Twins Discordant for Orofacial Clefts"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2239-8120","authenticated-orcid":false,"given":"A. L.","family":"Petrin","sequence":"first","affiliation":[{"name":"University of Iowa College of Dentistry and Dental Clinics, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-3548-7839","authenticated-orcid":false,"given":"H. L.","family":"Keen","sequence":"additional","affiliation":[{"name":"University of Iowa Carver College of Medicine, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0394-2126","authenticated-orcid":false,"given":"L.","family":"Dunlay","sequence":"additional","affiliation":[{"name":"University of Iowa College of Dentistry and Dental Clinics, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"X. J.","family":"Xie","sequence":"additional","affiliation":[{"name":"Florida State University College of Medicine, Tallahassee, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2891-6497","authenticated-orcid":false,"given":"E.","family":"Zeng","sequence":"additional","affiliation":[{"name":"University of Iowa College of Dentistry and Dental Clinics, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1229-5964","authenticated-orcid":false,"given":"A.","family":"Butali","sequence":"additional","affiliation":[{"name":"University of Iowa College of Dentistry and Dental Clinics, Iowa City, IA, USA"},{"name":"University of Iowa Carver College of Medicine, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3376-1311","authenticated-orcid":false,"given":"A.","family":"Wilcox","sequence":"additional","affiliation":[{"name":"Epidemiology Branch of the National Institute of Environmental Health Sciences, Durham, NC, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2648-2832","authenticated-orcid":false,"given":"M. L.","family":"Marazita","sequence":"additional","affiliation":[{"name":"University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2330-6398","authenticated-orcid":false,"given":"J. C.","family":"Murray","sequence":"additional","affiliation":[{"name":"University of Iowa Carver College of Medicine, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3408-4818","authenticated-orcid":false,"given":"L. M.","family":"Moreno-Uribe","sequence":"additional","affiliation":[{"name":"University of Iowa College of Dentistry and Dental Clinics, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"issue":"Suppl 7","key":"2026041012250490000_2026.04.07.26350251v1.1","first-page":"S11","article-title":"Global Birth Prevalence of Orofacial Clefts: A Systematic Review","volume":"98","year":"2015","journal-title":"J. Med. Assoc. Thai"},{"key":"2026041012250490000_2026.04.07.26350251v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2933"},{"key":"2026041012250490000_2026.04.07.26350251v1.3","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.c.31381"},{"key":"2026041012250490000_2026.04.07.26350251v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/ng.580"},{"key":"2026041012250490000_2026.04.07.26350251v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2360"},{"key":"2026041012250490000_2026.04.07.26350251v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/nature05918"},{"key":"2026041012250490000_2026.04.07.26350251v1.7","first-page":"636","article-title":"The genetic basis of craniofacial and dental abnormalities","volume":"121","year":"2011","journal-title":"Schweiz. Monatsschr. Zahnmed"},{"key":"2026041012250490000_2026.04.07.26350251v1.8","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.c.31375"},{"key":"2026041012250490000_2026.04.07.26350251v1.9","doi-asserted-by":"publisher","DOI":"10.1158\/1055-9965.Epi-13-1256"},{"key":"2026041012250490000_2026.04.07.26350251v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddx290."},{"key":"2026041012250490000_2026.04.07.26350251v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-02721-0"},{"key":"2026041012250490000_2026.04.07.26350251v1.12","doi-asserted-by":"publisher","DOI":"10.1080\/15592294.2019.1581591"},{"key":"2026041012250490000_2026.04.07.26350251v1.13","doi-asserted-by":"publisher","DOI":"10.1177\/10556656241269495"},{"key":"2026041012250490000_2026.04.07.26350251v1.14","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2021.656865"},{"key":"2026041012250490000_2026.04.07.26350251v1.15","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2012-13-10-172"},{"key":"2026041012250490000_2026.04.07.26350251v1.16","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3243"},{"key":"2026041012250490000_2026.04.07.26350251v1.17","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddx441"},{"key":"2026041012250490000_2026.04.07.26350251v1.18","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-026-03947-w"},{"key":"2026041012250490000_2026.04.07.26350251v1.19","doi-asserted-by":"publisher","DOI":"10.1002\/bdra.20709"},{"key":"2026041012250490000_2026.04.07.26350251v1.20","doi-asserted-by":"publisher","DOI":"10.1242\/dev.065938"},{"key":"2026041012250490000_2026.04.07.26350251v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2011.06.007"},{"key":"2026041012250490000_2026.04.07.26350251v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2014.11.031"},{"key":"2026041012250490000_2026.04.07.26350251v1.23","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.26.15002"},{"key":"2026041012250490000_2026.04.07.26350251v1.24","doi-asserted-by":"publisher","DOI":"10.1038\/78119"},{"key":"2026041012250490000_2026.04.07.26350251v1.25","doi-asserted-by":"publisher","DOI":"10.1038\/nrm3932"},{"key":"2026041012250490000_2026.04.07.26350251v1.26","doi-asserted-by":"publisher","DOI":"10.1016\/j.reprotox.2025.109030"},{"key":"2026041012250490000_2026.04.07.26350251v1.27","doi-asserted-by":"publisher","DOI":"10.1177\/00220345211062049"},{"key":"2026041012250490000_2026.04.07.26350251v1.28","doi-asserted-by":"publisher","DOI":"10.1093\/jn\/134.11.3106"},{"key":"2026041012250490000_2026.04.07.26350251v1.29","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM199511233332101"},{"key":"2026041012250490000_2026.04.07.26350251v1.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.12.041"},{"key":"2026041012250490000_2026.04.07.26350251v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2018.03.129"},{"key":"2026041012250490000_2026.04.07.26350251v1.32","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-40363-1"},{"key":"2026041012250490000_2026.04.07.26350251v1.33","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2016.02.019"},{"key":"2026041012250490000_2026.04.07.26350251v1.34","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-2-r31"},{"key":"2026041012250490000_2026.04.07.26350251v1.35","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky691"},{"key":"2026041012250490000_2026.04.07.26350251v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0213-x"},{"key":"2026041012250490000_2026.04.07.26350251v1.37","doi-asserted-by":"publisher","DOI":"10.21105\/joss.00861"},{"key":"2026041012250490000_2026.04.07.26350251v1.38","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007"},{"key":"2026041012250490000_2026.04.07.26350251v1.39","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-3808-1"},{"key":"2026041012250490000_2026.04.07.26350251v1.40","doi-asserted-by":"publisher","DOI":"10.1038\/srep16923"},{"key":"2026041012250490000_2026.04.07.26350251v1.41","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1630"},{"key":"2026041012250490000_2026.04.07.26350251v1.42","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003118"},{"key":"2026041012250490000_2026.04.07.26350251v1.43","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1597-8"},{"key":"2026041012250490000_2026.04.07.26350251v1.44","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229102. Article published online before print in May 2002"},{"key":"2026041012250490000_2026.04.07.26350251v1.45","doi-asserted-by":"publisher","DOI":"10.1016\/j.ydbio.2017.03.025"},{"key":"2026041012250490000_2026.04.07.26350251v1.46","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2008.211"},{"key":"2026041012250490000_2026.04.07.26350251v1.47","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx1132"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.04.07.26350251","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T19:25:14Z","timestamp":1775849114000},"score":1,"resource":{"primary":{"URL":"http:\/\/medrxiv.org\/lookup\/doi\/10.64898\/2026.04.07.26350251"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,8]]},"references-count":47,"URL":"https:\/\/doi.org\/10.64898\/2026.04.07.26350251","relation":{},"subject":[],"published":{"date-parts":[[2026,4,8]]},"subtype":"preprint"}}