Epigenetic inheritance is fundamental to human development and disease, yet the mechanisms governing the transmission of DNA methylation across generations remain incompletely understood. In this study, we performed haplotype-resolved, whole-genome DNA methylation profiling in a healthy three-generation Chinese family, leveraging high-depth Oxford Nanopore Technologies (ONT) and PacBio HiFi long-read sequencing, anchored to a proband-specific telomere-to-telomere (T2T) genome assembly. We observed globally conserved, bimodal methylation landscapes across all individuals and generations, with high concordance between corresponding parental and offspring haplotypes. Stratified analyses revealed functional compartmentalization of methylation marks, with distinct hypomethylation in gene bodies and centromeres and hypermethylation in retrotransposons and repetitive elements. Haplotype-resolved analysis of the X chromosome highlighted sex- and allele-specific methylation patterns linked to X inactivation dynamics. Together, this pedigree-scale, high-resolution study delineates the landscape and principles of intergenerational DNA methylation inheritance, revealing both conserved and dynamic features shaping the human epigenome.
All raw sequencing data are deposited in the China National Center for Bioinformation (CNCB) Genome Sequence Archive (GSA) database with the accession number HRA023802 under the BioProject ID PRJCA053156.