Atlas of imprinted and allele-specific DNA methylation in the human body

Jonathan Rosenski, Ayelet Peretz, Judith Magenheim, Netanel Loyfer, Ruth Shemer, Benjamin Glaser, Yuval Dor () and Tommy Kaplan ()
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Jonathan Rosenski: The Hebrew University of Jerusalem
Ayelet Peretz: The Hebrew University of Jerusalem
Judith Magenheim: The Hebrew University of Jerusalem
Netanel Loyfer: The Hebrew University of Jerusalem
Ruth Shemer: The Hebrew University of Jerusalem
Benjamin Glaser: The Hebrew University of Jerusalem
Yuval Dor: The Hebrew University of Jerusalem
Tommy Kaplan: The Hebrew University of Jerusalem

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Allele-specific DNA methylation reflects genetic variation and parentally-inherited changes, and is involved in gene regulation and pathologies. Yet, our knowledge of this phenomenon is largely limited to blood. Here we present a comprehensive atlas of allele-specific DNA methylation using deep whole-genome sequencing across 39 normal human cell types. We identified 325k regions, covering 6% of the genome and 11% of CpGs, that show a bimodal distribution of methylated and unmethylated molecules. In 34k of these regions, genetic variations at individual alleles segregate with methylation patterns, validating allele-specific methylation. We also identified 460 regions showing parental allele-specific methylation, the majority of which are novel, as well as 78 regions associated with known imprinted genes. Surprisingly, sequence-dependent and parental allele-dependent methylation is often restricted to specific cell types, revealing unappreciated variation of allele-specific methylation across the human body. Finally, we validate tissue-specific, maternal allele-specific methylation of CHD7, offering a potential mechanism for the paternal bias in the inheritance mode of CHARGE syndrome associated with this gene. The atlas provides a resource for studying allele-specific methylation and regulatory mechanisms underlying imprinted expression in specific human cell types.

Date: 2025
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DOI: 10.1038/s41467-025-57433-1

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