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Diverse endogenous retroviruses generate structural variation between human genomes via LTR recombination

Jainy Thomas, Hervé Perron, Cédric Feschotte
doi: https://doi.org/10.1101/382630
Jainy Thomas
1Department of Human Genetics, University of Utah School of Medicine, 15 North 2030 East, Rm 5100, Salt Lake City, UT 84112, USA, (801) 585-3385,
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  • For correspondence: jainyt@genetics.utah.edu
Hervé Perron
2GeNeuro, Plan-les-Ouates, Geneva, Switzerland,
3Université Claude Bernard, Lyon, France
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  • For correspondence: hperron@geneuro.com
Cédric Feschotte
4Department of Molecular Biology and Genetics, 107 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA, (607) 255-8793,
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  • For correspondence: cf458@cornell.edu
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ABSTRACT

Human endogenous retroviruses (HERVs) occupy a substantial fraction of the genome and impact cellular function with both beneficial and deleterious consequences. The vast majority of HERV sequences descend from ancient retroviral families no longer capable of infection or genomic propagation. In fact, most are no longer represented by full-length proviruses but by solitary long terminal repeats (solo LTRs) that arose via non-allelic recombination events between the two LTRs of a proviral insertion. Because LTR-LTR recombination events may occur long after proviral insertion but are challenging to detect in resequencing data, we hypothesize that this mechanism produces an underappreciated amount of genomic variation in the human population. To test this idea, we develop a computational pipeline specifically designed to capture such dimorphic HERV alleles from short-read genome sequencing data. When applied to 279 individuals sequenced as part of the Simons Genome Diversity Project, the pipeline retrieves most of the dimorphic variants previously reported for the HERV-K(HML2) subfamily as well as dozens of additional candidates, including members of the HERV-H and HERV-W families. We experimentally validate several of these candidates, including the first reported instance of an unfixed HERV-W provirus. These data indicate that human proviral content exhibit more extensive interindividual variation than previously recognized. These findings have important implications for our understanding of the contribution of HERVs to human physiology and disease.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 01, 2018.
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Diverse endogenous retroviruses generate structural variation between human genomes via LTR recombination
Jainy Thomas, Hervé Perron, Cédric Feschotte
bioRxiv 382630; doi: https://doi.org/10.1101/382630
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Diverse endogenous retroviruses generate structural variation between human genomes via LTR recombination
Jainy Thomas, Hervé Perron, Cédric Feschotte
bioRxiv 382630; doi: https://doi.org/10.1101/382630

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