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Over half of cases remain unexplained (uRPL) as paternal factors are rarely clinically evaluated or studied. This study presents data showing that sperm DNA methylation is a putative contributor to RPL. Using ONT direct whole methylome sequencing, we generated the largest cohort of locus-resolved, single-molecule sperm methylome maps from men with uRPL. We identified 294 differentially methylated regions (DMRs), of which 158 (53.7%) overlapped AluY repetitive elements, representing significant enrichment (z=40.9); most were hypomethylated in uRPL sperm and spanned the full length of individual AluY insertions. Because of single-molecule resolution, we show that the methylation differences found in uRPL sperm occur in a subpopulation of sperm rather than a uniform DNA methylation change across all sperm. AluY epimutation represents a previously unrecognized, predominant signature of paternal epigenetic perturbation in uRPL, establishing repetitive elements as a new axis of sperm epigenetic risk.<\/jats:p>","DOI":"10.64898\/2026.09.24.753615","type":"posted-content","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T11:50:11Z","timestamp":1790337011000},"source":"Crossref","is-referenced-by-count":0,"title":["Sperm AluY Epimutations in Male Partners of Couples with Unexplained Recurrent Pregnancy Loss"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0359-1112","authenticated-orcid":false,"given":"Elango","family":"Kamaraj","sequence":"first","affiliation":[{"name":"Department of Obstetrics and Gynecology, University of Texas Health, San Antonio, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordan","family":"Moore","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mykle","family":"Keni","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Terry","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nastaran","family":"Salehisedeh","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3646-9079","authenticated-orcid":false,"given":"Neha","family":"Biju","sequence":"additional","affiliation":[{"name":"Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6480-2000","authenticated-orcid":false,"given":"Martha","family":"Susiarjo","sequence":"additional","affiliation":[{"name":"Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1190-6302","authenticated-orcid":false,"given":"Jonathon","family":"Hill","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1171-4482","authenticated-orcid":false,"given":"Timothy","family":"Jenkins","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4885-4446","authenticated-orcid":false,"given":"Winifred","family":"Mak","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, University of Texas Health, San Antonio, TX, USA"},{"name":"Women\u2019s Health, Dell Medical School, University of Texas, Austin, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092906551837000_2026.09.24.753615v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.fertnstert.2026.03.001"},{"key":"2026092906551837000_2026.09.24.753615v1.2","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1097\/AOG.0000000000000859","article-title":"A national survey on public perceptions of miscarriage","volume":"125","year":"2015","journal-title":"Obstet. 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