Haplotype-resolved methylation profiling across three generations reveals principles of human epigenetic inheritance

Hongling Zhou; Weixue Mu; Jinjin Xu; Xin Bai; Yang Zhou; Ao Lan; Bo Wu; Lei Nie; Xia Shen; Chentao Yang; Linzhou Li; Yanni Song; Dongya Wu; Guangji Chen; Hailin Liu; Xiaobo Wang; Xin Jin; Chuanle Xiao; Guojie Zhang; Stephen Kwok-Wing Tsui; Jue Ruan

doi:10.1016/j.jgg.2026.03.011

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Haplotype-resolved methylation profiling across three generations reveals principles of human epigenetic inheritance

doi: 10.1016/j.jgg.2026.03.011

Funds:

the High-quality Science and Technology Journal Construction Project of Guangdong Province (2025B1212100003 and 2025B1212070003)

This work was supported by grants from the National Key R &

and research grants from Hong Kong SAR, including the Collaborative Research Grant (C4049-23EF) and Theme-based Research Scheme (T12-716/22-R and T11-709/21-N) from the Research Grants Council of the Hong Kong SAR.Thanks to Wenjing Wei and Long Zhou from Zhejiang University for their support in data transfer and server use and Yafei Mao from Shanghai Jiao Tong University for his guidance on data analysis. Thanks also for the support from the Innovation Program of the Chinese Academy of Agricultural Sciences and the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202503).

D Program of China (2025YFC3410300)

Received Date: 2025-12-14
Accepted Date: 2026-03-13
Rev Recd Date: 2026-03-12

Available Online: 2026-03-30

Abstract

Abstract

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. Stratified analyses revealed clear functional compartmentalization of methylation marks, characterized by distinct hypomethylation in centromeres and hypermethylation in retrotransposons and repetitive elements. Chromosome-resolved analysis of ribosomal DNA (rDNA) arrays demonstrated a domain-specific methylation pattern with hypomethylation in the transcriptional core and hypermethylation in the intergenic spacer, with evidence for age-associated epigenetic drift in the transcriptional core domain. Through de novo identification and validation, we mapped 23 high-confidence imprinting control regions (ICRs) showing robust parent-of-origin-specific methylation, all overlapping known imprinted genes and enriched for regulatory element signatures. Haplotype-resolved X chromosome analysis further uncovered 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.
- Epigenetic regulation,
- DNA methylation,
- haplotype resolution,
- pedigree,
- imprinted control region,
- transgenerational inheritance

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