{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T20:41:50Z","timestamp":1784839310336,"version":"3.55.0"},"posted":{"date-parts":[[2025,11,4]]},"group-title":"Genomics","reference-count":149,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T00:00:00Z","timestamp":1762214400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"National Institutes of Health National Institute of General Medical Sciences","award":["R35-GM151945"],"award-info":[{"award-number":["R35-GM151945"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,11,4]]},"abstract":"<jats:title>Summary<\/jats:title>\n                <jats:p>\n                  Non-canonical (non-B) DNA secondary structures, e.g., G-quadruplexes and triplex DNA, are mutation hotspots and genome regulators contributing to disease and evolution. Yet they remain uncharacterized in complete genomes\n                  <jats:italic>in vivo<\/jats:italic>\n                  . Here we exploited the fact that many non-B DNA structures form single-stranded DNA (ssDNA). Using permanganate\/S1 footprinting across 14 cell lines, we generated ssDNA profiles for human and six non-human ape telomere-to-telomere (T2T) genomes. Newly resolved satellite arrays\u2014e.g., at ribosomal DNA and centromeres\u2014displayed high ssDNA levels, implicating non-B DNA in satellite expansion and function. Hidden Markov Models applied to our ssDNA data revealed active genomic domains with specific functions\u2014e.g., replication, transcription, or recombination\u2014each enriched in particular non-B DNA types. Human-specific ssDNA domains correlated with nervous system genes, whereas cancer and embryonic cells showed increased ssDNA in transposable elements. Our ssDNA analysis across ape T2T genomes uncovered conserved and species-specific DNA structural dynamics central to genome regulation.\n                <\/jats:p>","DOI":"10.1101\/2025.11.03.686349","type":"posted-content","created":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T08:45:12Z","timestamp":1762332312000},"source":"Crossref","is-referenced-by-count":2,"title":["Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5414-1667","authenticated-orcid":false,"given":"Jacob","family":"Sieg","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiqing","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8803-9433","authenticated-orcid":false,"given":"Hana","family":"P\u00e1lov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8415-9259","authenticated-orcid":false,"given":"Linn\u00e9a","family":"Smeds","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1813-589X","authenticated-orcid":false,"given":"Saswat","family":"Mohanty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7402-3369","authenticated-orcid":false,"given":"Angelika","family":"Lahnsteiner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Chiaromonte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6212-9526","authenticated-orcid":false,"given":"Kateryna 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