{
  "abstract": "CpG dinucleotides are essential substrates for DNA methylation and genome regulation, yet paradoxically, methylated CpGs are lost through deamination-associated mutations. How CpG-rich sequences persist and are replenished during evolution remains unresolved, as previous sequencing technologies left structurally complex regions inaccessible. Here, leveraging complete telomere-to-telomere ape genomes, we show that peri/centromeric satellites are reservoirs of hypomethylated CpGs in sperm, and likely oocytes. This peri/centromeric hypomethylation extends into adjacent euchromatin, revealing novel centromeric hypomethylation extension domains enriched for segmental duplications, recently duplicated genes, and testis- and brain-biased expression. More broadly, young structural variants are CpG-rich and germline-hypomethylated, whereas older sequences are methylated and CpG-depleted. These findings link rapidly evolving centromeric regions to distinctive germline epigenetic state, CpG evolution, and structural and transcriptomic evolutionary innovation.",
  "abstract_shown": true,
  "affiliations": [
    "University of California, Santa Barbara"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "D. R. Son"
    },
    {
      "name": "E. Y.- H. Loh"
    },
    {
      "name": "H. Jeong"
    },
    {
      "name": "J. Ma"
    },
    {
      "name": "E. E. Eichler"
    },
    {
      "affs": [
        0
      ],
      "name": "S. V. Yi"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2szze69hhtv52.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.06.15.732472",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.06.15.732472v3.full",
  "id": "2szze69hhtv52",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.06.15.732472v3",
  "language": null,
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ],
    [
      "openalex",
      "1312|Epigenetics and DNA Methylation"
    ]
  ],
  "openalex": "W7165158006",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.06.15.732472v3.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-06-15",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/2szze69hhtv52.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:25:58Z",
      "native_id": "10.64898/2026.06.15.732472",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.06.15.732472v3"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes",
  "title_text": "Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes",
  "type": "preprint",
  "updated_at": "2026-10-30T12:25:58Z",
  "url": "https://research.draconitic.com/paper/2szze69hhtv52",
  "venue": "bioRxiv",
  "versions": []
}