{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T05:07:00Z","timestamp":1789880820947,"version":"4.0.1"},"posted":{"date-parts":[[2026,9,12]]},"group-title":"Genetics","reference-count":27,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T00:00:00Z","timestamp":1789171200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["K22CA177824"],"award-info":[{"award-number":["K22CA177824"]}],"id":[{"id":"https:\/\/ror.org\/040gcmg81","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R21CA259630"],"award-info":[{"award-number":["R21CA259630"]}],"id":[{"id":"https:\/\/ror.org\/040gcmg81","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Human acrocentric short arms harbor K111, an endogenous retrovirus that became an integral component of nucleolar organizer region (NOR)-associated architecture across all five acrocentric chromosome types. Here we combine complete human and primate genomes, haplotype-resolved population assemblies and parent-offspring trios to reconstruct its evolution and transmission. Predominantly full-length ancestral elements underwent human-specific expansion and remodeling, generating recurrent mosaics and individual-specific multicopy configurations. Population structural variation is concentrated in surrounding satellite landscapes rather than within K111-derived sequences themselves. Trio-resolved genomes reveal direct parental transmission, single-parent remodeling and, crucially, maternal-paternal remodeling in distinct configurations: large reciprocal domains with contrasting parental affinities and de novo sequence exchange within an offspring locus. Raw long reads support both maternal-paternal configurations. K111-derived loci associate with nucleolin-positive compartments. Together, these findings establish K111 as an evolutionarily dynamic component and molecular record of acrocentric NOR architecture, revealing unrecognized remodeling and sequence generation across human generations.<\/jats:p>","DOI":"10.64898\/2026.09.11.751073","type":"posted-content","created":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T11:55:11Z","timestamp":1789214111000},"source":"Crossref","is-referenced-by-count":0,"title":["Human-specific remodeling of an endogenous retrovirus shapes structural diversity at acrocentric nucleolar organizer regions"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1708-0137","authenticated-orcid":false,"given":"Mohammad","family":"Waseem","sequence":"first","affiliation":[{"name":"Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35233"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5031-5607","authenticated-orcid":false,"given":"Amit","family":"Datta","sequence":"additional","affiliation":[{"name":"Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35233"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hudson","family":"O\u2019Neill","sequence":"additional","affiliation":[{"name":"Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35233"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-6447-7682","authenticated-orcid":false,"given":"Azait","family":"Imtiaz","sequence":"additional","affiliation":[{"name":"Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35233"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6284-3359","authenticated-orcid":false,"given":"Rafael","family":"Contreras-Galindo","sequence":"additional","affiliation":[{"name":"Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35233"},{"name":"Division of Clinical Immunology and Rheumatology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35233"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026091921351139000_2026.09.11.751073v3.1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj6987"},{"key":"2026091921351139000_2026.09.11.751073v3.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05896-x"},{"key":"2026091921351139000_2026.09.11.751073v3.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05976-y"},{"key":"2026091921351139000_2026.09.11.751073v3.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-08816-3"},{"key":"2026091921351139000_2026.09.11.751073v3.5","doi-asserted-by":"crossref","first-page":"4876","DOI":"10.1016\/j.cell.2026.05.035","article-title":"Human acrocentric chromosome short-arm de novo mutation and recombination","volume":"189","year":"2026","journal-title":"Cell"},{"key":"2026091921351139000_2026.09.11.751073v3.6","doi-asserted-by":"publisher","DOI":"10.1101\/gr.144303.112"},{"key":"2026091921351139000_2026.09.11.751073v3.7","doi-asserted-by":"crossref","unstructured":"Zahn, J. et al. 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