Endogenous retroviruses in mammals: An emerging picture of how ERVs modify expression of adjacent genes

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216 · see citing works

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129 · see citing works

Mouse genomic variation and its effect on phenotypes and gene regulation.

Keane, T. M., Goodstadt, L., Danecek, P., White, M. A., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., et al. (2011) · Nature · doi:10.1038/nature10413 · Cited by 1,580 · see citing works

The Mouse Locus Encodes Axin, an Inhibitor of the Wnt Signaling Pathway That Regulates Embryonic Axis Formation

Zeng, L., Fagotto, F., Zhang, T., Hsu, W., Vasicek, T. J., Perry, W. L., Lee, J. J., Tilghman, S. M., Gumbiner, B. M., & Costantini, F. D. (1997) · Cell · doi:10.1016/s0092-8674(00)80324-4 · Cited by 907 · see citing works

Somatic retrotransposition alters the genetic landscape of the human brain

Baillie, J. K., Barnett, M. W., Upton, K. R., Gerhardt, D. J., Richmond, T. A., De Sapio, F., Brennan, P. M., Rizzu, P., Smith, S., Fell, M., et al. (2011) · Nature · doi:10.1038/nature10531 · Cited by 684 · see citing works

Transgenerational inheritance of epigenetic states at the murine Axin Fu allele occurs after maternal and paternal transmission

Rakyan, V. K., Chong, S., Blewitt, M. E., Cuthbert, P. C., Morgan, H. D., Luu, K. V. K., & Whitelaw, E. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0436776100 · Cited by 642 · see citing works

LINE-1 Retrotransposition Activity in Human Genomes

Beck, C. R., Collier, P., Macfarlane, C., Malig, M., Kidd, J. M., Eichler, E. E., Badge, R. M., & Moran, J. V. (2010) · Cell · doi:10.1016/j.cell.2010.05.021 · Cited by 632 · see citing works

Active human retrotransposons: variation and disease

Hancks, D. C., & Kazazian, H. H. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.02.006 · Cited by 592 · see citing works

Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes

Han, J. S., Szak, S. T., & Boeke, J. D. (2004) · Nature · doi:10.1038/nature02536 · Cited by 484 · see citing works

Neomorphic agouti mutations in obese yellow mice

Duhl, D. M. J., Vrieling, H., Miller, K. A., Wolff, G. L., & Barsh, G. S. (1994) · Nature Genetics · doi:10.1038/ng0994-59 · Cited by 448 · see citing works

CONTROLLING ELEMENTS IN MAIZE

Fincham, J. R. S., & Sastry, G. R. K. (1974) · Annual Review of Genetics · doi:10.1146/annurev.ge.08.120174.000311 · Cited by 405 · see citing works

Biased chromatin signatures around polyadenylation sites and exons

Nielsen, C. B., Padgett, R. A., Spies, N., & Burge, C. B. (2009) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 390 · see citing works

A comprehensive map of mobile element insertion polymorphisms in humans

Stewart, C., Kural, D., Strömberg, M. P., Walker, J. A., Konkel, M. K., Stütz, A. M., Urban, A. E., Grubert, F., Lam, H. Y. K., Lee, W.-P., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002236 · Cited by 307 · see citing works

Sequence-based characterization of structural variation in the mouse genome

Yalcin, B., Wong, K., Agam, A., Goodson, M., Keane, T. M., Gan, X., Nellåker, C., Goodstadt, L., Nicod, J., Bhomra, A., et al. (2011) · Nature · doi:10.1038/nature10432 · Cited by 301 · see citing works

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomesPreprint

Ewing, A. D., & Kazazian, H. H. (2010) · Genome Research · doi:10.1101/gr.106419.110 · Cited by 301 · see citing works

Unravelling the means to an end: RNA polymerase II transcription termination

Kuehner, J. N., Pearson, E. L., & Moore, C. L. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3098 · Cited by 299 · see citing works

Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage.Preprint

Michaud, E. J., van Vugt, M. J., Bultman, S. J., Sweet, H. O., Davisson, M. T., & Woychik, R. P. (1994) · Genes & Development · doi:10.1101/gad.8.12.1463 · Cited by 279 · see citing works

Two Dominant Mutations in the Mouse Fused Gene Are the Result of Transposon Insertions

Vasicek, T. J., Zeng, L., Guan, X.-J., Zhang, T., Costantini, F. D., & Tilghman, S. M. (1997) · Genetics · doi:10.1093/genetics/147.2.777 · Cited by 167 · see citing works

Regulation of alternative polyadenylation by genomic imprintingPreprint

Wood, A. J., Schulz, R., Woodfine, K., Koltowska, K., BEECHEY, C. V., Peters, J., Bourc’his, D., & Oakey, R. J. (2008) · Genes & Development · doi:10.1101/gad.473408 · Cited by 163 · see citing works

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

Rebollo, R., Karimi, M. M., Bilenky, M., Gagnier, L., Miceli-Royer, K., Zhang, Y., Goyal, P., Keane, T., Jones, S. J. M., Hirst, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002301 · Cited by 157 · see citing works

A Role for Chromatin Remodeling in Transcriptional Termination by RNA Polymerase II

Amaro, C. A., Kent, N. A., Jones, H. S., O'Sullivan, J. M., Aranda, A., & Proudfoot, N. J. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00778-5 · Cited by 157 · see citing works

Complex patterns of transcription at the insertion site of a retrotransposon in the mouse

Druker, R. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh914 · Cited by 110 · see citing works

Phenotypic and molecular analysis of a transgenic insertional allele of the mouse Fused locus.

Perry, W. L., Vasicek, T. J., Lee, J.-J., Rossi, J. M., Zeng, L., Zhang, T., Tilghman, S. M., & Costantini, F. D. (1995) · Genetics · doi:10.1093/genetics/141.1.321 · Cited by 103 · see citing works

Mobile elements in the human genome: implications for disease

Sólyom, S., & Kazazian, H. H. (2012) · Genome Medicine · doi:10.1186/gm311 · Cited by 97 · see citing works

Molecular Basis of the Pleiotropic Phenotype of Mice Carrying the hypervariable yellow (Ahvy) Mutation at the agouti Locus

Argeson, A. C., Nelson, K. K., & Siracusa, L. D. (1996) · Genetics · doi:10.1093/genetics/142.2.557 · Cited by 79 · see citing works

Mosaicism of tyrosinase‐locus transcription and chromatin structure in dark vs. light melanocyte clones of homozygous chinchilla‐mottled mice

Porter, S. D., Larue, L., & Mintz, B. (1991) · Developmental Genetics · doi:10.1002/dvg.1020120604 · Cited by 59 · see citing works

Design principles of interconnections between chromatin and pre-mRNA splicing

de Almeida, S. F., & Carmo‐Fonseca, M. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2012.02.002 · Cited by 56 · see citing works

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distancePreprint

Li, J., Akagi, K., Hu, Y., Trivett, A. L., Hlynialuk, C. J. W., Swing, D. A., Volfovsky, N., Morgan, T. C., Golubeva, Y. G., Stephens, R. M., et al. (2012) · Genome Research · doi:10.1101/gr.130740.111 · Cited by 52 · see citing works

The molecular basis for dominant yellow agouti coat color mutations

Perry, W. L., Copeland, N. G., & Jenkins, N. A. (1994) · BioEssays · doi:10.1002/bies.950161002 · Cited by 45 · see citing works

Inherited somatic mosaicism caused by an intracisternal A particle insertion in the mouse tyrosinase gene

Wu, M., Rinchik, E. M., Wilkinson, E., & Johnson, D. K. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.3.890 · Cited by 32 · see citing works

Alternative splicing and expressivity of the AxinFu allele in mice

Flood, W. D., & Ruvinsky, A. O. (2001) · Heredity · doi:10.1046/j.1365-2540.2001.00868.x · Cited by 16 · see citing works

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

Thompson, P. J., Macfarlan, T. S., & Lorincz, M. C. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.03.029 · Cited by 301 · see citing works

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells

Fasching, L., Kapopoulou, A., Sachdeva, R., Petri, R., Jönsson, M. E., Männe, C., Turelli, P., Jern, P., Cammas, F., Trono, D., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.12.004 · Cited by 138 · see citing works

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

Geering, A. D. W., Maumus, F., Copetti, D., Choisne, N., Zwickl, D. J., Zytnicki, M., McTaggart, A. R., Scalabrin, S., Vezzulli, S., Wing, R. A., et al. (2014) · Nature Communications · doi:10.1038/ncomms6269 · Cited by 129 · see citing works

Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes

Grandi, N., Cadeddu, M., Blomberg, J., & Tramontano, E. (2016) · Retrovirology · doi:10.1186/s12977-016-0301-x · Cited by 93 · see citing works

Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis

Young, G. R., Stoye, J. P., & Kassiotis, G. (2013) · BioEssays · doi:10.1002/bies.201300049 · Cited by 78 · see citing works

Endogenous Retroviruses Transcriptional Modulation After Severe Infection, Trauma and Burn

Tabone, O., Mommert, M., Jourdan, C., Cerrato, E., Legrand, M., Lepape, A., Allaouchiche, B., Rimmele, T., Pachot, A., Monneret, G., et al. (2018) · bioRxiv · doi:10.3389/fimmu.2018.03091 · Cited by 68 · see citing works

COVID-19 in Children: Expressions of Type I/II/III Interferons, TRIM28, SETDB1, and Endogenous Retroviruses in Mild and Severe Cases

Tovo, P.-A., Garazzino, S., Daprà, V., Pruccoli, G., Calvi, C., Mignone, F., Alliaudi, C., Denina, M., Scolfaro, C., Zoppo, M., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147481 · Cited by 58 · see citing works

A new look at the LTR retrotransposon content of the chicken genome

Mason, A. S., Fulton, J. E., Hocking, P. M., & Burt, D. W. (2016) · BMC Genomics · doi:10.1186/s12864-016-3043-1 · Cited by 45 · see citing works

Whole genome sequencing of Gyeongbuk Araucana, a newly developed blue-egg laying chicken breed, reveals its origin and genetic characteristics

Jeong, H., Kim, K., Caetano-Anollés, K., Kim, H., Kim, B.-K., Yi, J., Ha, J. J., Cho, S., & Oh, D. Y. (2016) · Scientific Reports · doi:10.1038/srep26484 · Cited by 34 · see citing works

Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data

Mason, A. S., Lund, A. R., Hocking, P. M., Fulton, J. E., & Burt, D. W. (2020) · Mobile DNA · doi:10.1186/s13100-020-00216-w · Cited by 29 · see citing works

Endogenous Retroviruses in Domestic Animals

García‐Etxebarria, K., Sistiaga-Poveda, M., & Jugo, B. M. (2014) · Current Genomics · doi:10.2174/1389202915666140520003503 · Cited by 24 · see citing works

Enhanced Expression of Human Endogenous Retroviruses, TRIM28 and SETDB1 in Autism Spectrum Disorder

Tovo, P., Davico, C., Marcotulli, D., Vitiello, B., Daprà, V., Calvi, C., Montanari, P., Carpino, A., Galliano, I., & Bergallo, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23115964 · Cited by 23 · see citing works

Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split

Gemmell, P., Hein, J., & Katzourakis, A. (2015) · Retrovirology · doi:10.1186/s12977-015-0172-6 · Cited by 19 · see citing works

Enhanced Transcription of Human Endogenous Retroviruses and TRIM28 Downregulation in Patients with Inflammatory Bowel Disease

Tovo, P., Ribaldone, D. G., Galliano, I., Caviglia, G. P., Dini, M., Veglio, V., Calvi, C., Montanari, P., Pitoni, D., Frara, S., et al. (2024) · Viruses · doi:10.3390/v16101570 · Cited by 19 · see citing works

How do mammalian transposons induce genetic variation? A conceptual framework

Akagi, K., Li, J., & Symer, D. E. (2013) · BioEssays · doi:10.1002/bies.201200133 · Cited by 19 · see citing works

Tracking the Fate of Endogenous Retrovirus Segregation in Wild and Domestic Cats

Ngo, M. H., Arnal, M. C., Sumi, R., Kawasaki, J., Miyake, A., Grant, C. K., Otoi, T., de Luco, D. F., & Nishigaki, K. (2019) · Journal of Virology · doi:10.1128/jvi.01324-19 · Cited by 17 · see citing works

Human Endogenous Retroviruses: Residues of Ancient Times Are Differentially Expressed in Crohn’s Disease

Klag, T., Courth, L. F., Ostaff, M. J., Ott, G., Stange, E. F., Malek, N. P., Seifarth, W., & Wehkamp, J. (2018) · Inflammatory Intestinal Diseases · doi:10.1159/000494026 · Cited by 14 · see citing works

Evolution of Endogenous Retroviruses in the Subfamily of Caprinae

Moawad, A. S., Wang, F., Zheng, Y., Chen, C., Saleh, A. A., Hou, J., & Song, C. (2024) · Viruses · doi:10.3390/v16030398 · Cited by 12 · see citing works

Enhanced expression of endogenous retroviruses and of TRIM28 and SETDB1 in children with food allergy

Tovo, P., Monti, G., Daprà, V., Montanari, P., Calvi, C., Alliaudi, C., Sardo, A., Galliano, I., & Bergallo, M. (2022) · Clinical and Translational Allergy · doi:10.1002/clt2.12124 · Cited by 10 · see citing works

Pregnancy Is Associated with Impaired Transcription of Human Endogenous Retroviruses and of TRIM28 and SETDB1, Particularly in Mothers Affected by Multiple Sclerosis

Tovo, P., Marozio, L., Abbona, G., Calvi, C., Frezet, F., Gambarino, S., Dini, M., Benedetto, C., Galliano, I., & Bergallo, M. (2023) · Viruses · doi:10.3390/v15030710 · Cited by 9 · see citing works

High Expression of Endogenous Retroviral Envelope Gene in the Equine Fetal Part of the Placenta

Stefanetti, V., Marenzoni, M. L., Passamonti, F., Cappelli, K., García‐Etxebarria, K., Coletti, M., & Capomaccio, S. (2016) · PLoS ONE · doi:10.1371/journal.pone.0155603 · Cited by 9 · see citing works

Expressions of Type I and III Interferons, Endogenous Retroviruses, TRIM28, and SETDB1 in Children with Respiratory Syncytial Virus Bronchiolitis

Tovo, P., Garazzino, S., Savino, F., Daprà, V., Pruccoli, G., Dini, M., Filisetti, G., Funiciello, E., Galliano, I., & Bergallo, M. (2023) · Current Issues in Molecular Biology · doi:10.3390/cimb45020079 · Cited by 8 · see citing works

Children with Chronic Immune Thrombocytopenia Exhibit High Expression of Human Endogenous Retroviruses TRIM28 and SETDB1

Tovo, P., Galliano, I., Parodi, E., Calvi, C., Gambarino, S., Licciardi, F., Dini, M., Montanari, P., Branca, M., Ramenghi, U., et al. (2023) · Genes · doi:10.3390/genes14081569 · Cited by 8 · see citing works

Impaired transcription of human endogenous retroviruses in the sperm with exception of syncytin 1: short communication

Bergallo, M., Canosa, S., Galliano, I., Daprà, V., Montanari, P., Sestero, M., Gennarelli, G., Benedetto, C., Revelli, A., & Tovo, P.-A. (2021) · Molecular Biology Reports · doi:10.1007/s11033-021-06577-6 · Cited by 6 · see citing works

Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus

Yang, L., Malhotra, R., Chikhi, R., Elleder, D., Kaiser, T., Rong, J., Medvedev, P., & Poss, M. L. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab252 · Cited by 6 · see citing works

Patients with Irritable Bowel Syndrome Exhibit Aberrant Expression of Endogenous Retroviruses and SETDB1

Tovo, P.-A., Ribaldone, D. G., Caviglia, G. P., Calvi, C., Montanari, P., Tizzani, M., Pitoni, D., Frara, S., Tribocco, E., Gambarino, S., et al. (2025) · Cells · doi:10.3390/cells14030196 · Cited by 4 · see citing works

Diversity, evolution, and gene regulation of endogenous retroviruses in eight important poultry species

Moawad, A. S., Omara, A., Wan, Z., Xie, Q., Shao, H., Qin, A., Li, T., & Ye, J. (2025) · Veterinary Microbiology · doi:10.1016/j.vetmic.2025.110596 · Cited by 2 · see citing works

Role of endogenous retrovirus promoter activity in tumor suppression

Krönung, S. K. (2015) · doi:10.53846/goediss-5097

Resposta imune contra HERV-K em pacientes com câncer de próstata localizado e metastático

Dzik, C. (2017) · doi:10.11606/t.5.2017.tde-14122017-105022

Aberrant Expression of Human Endogenous Retroviruses and SETDB1 in Adolescents with Anorexia Nervosa

Amianto, F., Tovo, P., Po, A., Calvi, C., Davico, C., Montanari, P., Rainò, E., Anichini, A., Vesco, S., Bechis, D., et al. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27093755

A Novel Genus of Endogenous Pararetroviruses with Long Terminal Repeats in GrassesPreprint

Gao, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.08.658526

Impact of Antiretroviral Treatment on the Expression of Human Endogenous Retrovirus in Mesenchymal Stem CellsPreprint

Dini, M., Galliano, I., Castagnoli, C., Clemente, A., Pau, A., Gambarino, S., Tovo, P., & Bergallo, M. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5347175

Burn-induced alterations in human endogenous retrovirus transcriptional activity in peripheral blood

Dini, M., ROMEO, M., Pau, A., Gambarino, S., Pensa, A., Clemente, A., Tovo, P.-A., Galliano, I., & Bergallo, M. (2025) · Minerva Biotechnology and Biomolecular Research · doi:10.23736/s2724-542x.25.03261-4

Discovery and Evolutionary Analysis of a Novel Genus of Endogenous Pararetroviruses with Long Terminal Repeats

Gao, D., & Tressel, L. G. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf237

Modulation de l'expression des rétrovirus endogènes humains dans des contextes d'inflammation et d'immunosuppression

Mommert, M. (2018) · theses.fr (ABES) · doi:10.70675/1abfa18dza023z4786z9253za64fea51a7ba

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distancePreprint

Li, J., Akagi, K., Hu, Y., Trivett, A. L., Hlynialuk, C. J. W., Swing, D. A., Volfovsky, N., Morgan, T. C., Golubeva, Y. G., Stephens, R. M., et al. (2012) · Genome Research · doi:10.1101/gr.130740.111 · Cited by 52 · see citing works

Endogenous Retroviruses: With Us and against Us

Meyer, T. J., Rosenkrantz, J. L., Carbone, L., & Chavez, S. L. (2017) · Frontiers in Chemistry · doi:10.3389/fchem.2017.00023 · Cited by 78 · see citing works

Transcriptional Regulation of Endogenous Retroviruses and Their Misregulation in Human Diseases

Zhang, Q., Pan, J., Cong, Y., & Mao, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231710112 · Cited by 25 · see citing works

Mammalian Endogenous Retroviruses

Mager, D. L., & Stoye, J. P. (2015) · ASM Press eBooks · doi:10.1128/9781555819217.ch47 · Cited by 16 · see citing works

Endogenous Retroviruses: Suspects in the Disease World

Singh, S. K. (2007) · Future Microbiology · doi:10.2217/17460913.2.3.269 · Cited by 14 · see citing works