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Adv."],"published-print":{"date-parts":[[2026,6,19]]},"abstract":"<jats:p>Epigenetic dysregulation plays an essential role in autism spectrum disorder (ASD), but the parent-of-origin effects (POEs) of DNA methylation remain unknown. Here, we applied PacBio HiFi sequencing with haplotype-phased methylation profiling in 124 individuals (31 ASD quartets) to systematically dissect POE-dependent methylation. Comparative analysis of phased methylomes between probands and unaffected siblings identified 114 paternal- and 106 maternal-specific differential methylated cytosines (DMCs), 45 and 46 differential methylated regions (DMRs), and 2425 and 2693 methylation outliers (MOs), respectively. These POE methylation alterations were enriched in ASD-relevant gene categories but exhibited distinct genomic distributions and functional pathways between parental haplotypes. Furthermore, genome-wide parent-of-origin DMR analysis identified 443 allele-specific methylation (ASM) regions, from which we detected 34 differential expression ASMs and 62 ASM outliers, showing pronounced enrichment within PWS\/AS locus and ASD-associated genes. Collectively, this study provides a comprehensive evidence of pervasive POE-dependent methylation imbalance and aberrant ASM at imprinting regions underlying ASD pathogenesis, offering insights into epigenetic mechanisms of complex neurodevelopmental disorders.<\/jats:p>","DOI":"10.1126\/sciadv.aee4069","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T18:00:26Z","timestamp":1781719226000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":0,"title":["Haplotype-resolved methylomes reveal parent-of-origin DNA methylation imbalance in autism spectrum disorder"],"prefix":"10.1126","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2450-1320","authenticated-orcid":true,"given":"Lu","family":"Xia","sequence":"first","affiliation":[{"name":"Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008 Hunan, China."},{"name":"The Key Laboratory of Pediatric Rare Diseases of the Ministry of Education, University of South China, Hengyang and Central South University, Changsha, 410078 Hunan, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7645-189X","authenticated-orcid":true,"given":"Hailiang","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Public Health, Peking University, Beijing 100191, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7397-3848","authenticated-orcid":true,"given":"Ruiting","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008 Hunan, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-4227-7368","authenticated-orcid":true,"given":"Xue","family":"Ren","sequence":"additional","affiliation":[{"name":"Annoroad Gene Technology (Beijing) Co. 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