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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.<\/jats:p>","DOI":"10.64898\/2026.06.15.732472","type":"posted-content","created":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T08:50:11Z","timestamp":1781859011000},"source":"Crossref","is-referenced-by-count":0,"title":["Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-6806-7258","authenticated-orcid":false,"given":"Dongmin R.","family":"Son","sequence":"first","affiliation":[{"name":"Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara; Santa Barbara, CA, USA"},{"name":"Neuroscience Research Institute, University of California Santa Barbara; Santa Barbara, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6185-9279","authenticated-orcid":false,"given":"Eddie Y.-H.","family":"Loh","sequence":"additional","affiliation":[{"name":"Neuroscience Research Institute, University of California Santa Barbara; Santa Barbara, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5565-2685","authenticated-orcid":false,"given":"Hyeonsoo","family":"Jeong","sequence":"additional","affiliation":[{"name":"Neuroscience Research Institute, University of California Santa Barbara; Santa Barbara, CA, USA"},{"name":"Department of Life Sciences, Gwangju Institute of Science and Technology; Gwangju, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4202-5834","authenticated-orcid":false,"given":"Jian","family":"Ma","sequence":"additional","affiliation":[{"name":"Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8246-4014","authenticated-orcid":false,"given":"Evan E.","family":"Eichler","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA"},{"name":"Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1497-1871","authenticated-orcid":false,"given":"Soojin V.","family":"Yi","sequence":"additional","affiliation":[{"name":"Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara; Santa Barbara, CA, USA"},{"name":"Neuroscience Research Institute, University of California Santa Barbara; Santa Barbara, CA, USA"},{"name":"Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara; Santa Barbara, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026100808550863000_2026.06.15.732472v3.1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.947102"},{"key":"2026100808550863000_2026.06.15.732472v3.2","first-page":"484","article-title":"Functions of DNA methylation: islands, start sites, gene bodies and beyond","volume":"201","year":"2012","journal-title":"Nat. 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