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bioRxiv · 10.64898/2026.09.11.751073

Human-specific remodeling of an endogenous retrovirus shapes structural diversity at acrocentric nucleolar organizer regions

WASEEM, M.·Datta, A.·Imtiaz, A.·O Neill, H.·Galindo, R. C.
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Abstract

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.

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WASEEM, M., Datta, A., Imtiaz, A., O Neill, H., Galindo, R. C.. 2026-09-12. Human-specific remodeling of an endogenous retrovirus shapes structural diversity at acrocentric nucleolar organizer regions. https://doi.org/10.64898/2026.09.11.751073

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