221: Allele-resolved nanopore tour of the human placental methylome

️ Episode 221: Allele-resolved nanopore tour of the human placental methylome In this episode of PaperCast Base by Base, we explore Using phased long-read nanopore and short-read sequencing across eight trios, the study maps allele-specific DNA methylation and transcription in female human placentas, identifies hundreds of DMRs and novel imprinted genes, and reports somatic placental variants Study Highlights:The authors combined >20x Oxford Nanopore whole-genome sequencing with Illumina WGS and RNA-seq in eight mother–father–placenta trios to phase reads into maternal and paternal alleles. They catalogued 723 differentially methylated regions, finding a strong bias toward paternal demethylation concentrated in partially methylated domains. Allele-resolved expression analysis identified 74 imprinted genes and revealed previously unreported imprinted loci including paternally expressed ILDR2 and maternally expressed RASA1. The study also detected widespread somatic point mutations and a small number of placenta-specific structural variants, including a CNDP1–ZNF407 duplication associated with altered gene expression Conclusion:Phased nanopore sequencing provides a high-resolution, allele-specific map of the placental methylome and transcriptome, revealing novel imprinted genes and somatic variation with potential relevance to placental biology Music:Enjoy the music based on this article at the end of the episode. Reference:Kindlova M, Byrne H, Kubler JM, Steane SE, Whyte JM, Borg D, Clifton VL & Ewing AD. An allele-resolved nanopore-guided tour of the human placental methylome. Nat Commun. 2025;16:10358. https://doi.org/10.1038/s41467-025-65337-3 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com Castos player https://basebybase.castos.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

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