Coffin J.M., Hughes S.H. & Varmus H.E. (1997). - The interactions of retroviruses and their hosts. In Retroviruses (J.M. Coffin, S.H. Hughes & H.E. Varmus, eds). Cold Spring Harbor, New York.
Holmes E.C. (2011). - The evolution of endogenous viral elements. Cell Host Microbe, 10 (4), 368-377. doi: 10.1016/j. chom.2011.09.002.
Belyi VA., Levine A.J. & Skalka A.M. (2010). - Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the Parvoviridae and Circoviridae art more than 40 to 50 million years old. J. Virol, 84 (23), 12458-12462. doi:10.1128/JVI.01789-10.
Arbuckle J.H., Medveczky M.M., Luka J., Hadley S.H., Luegmayr A., Ablashi D., Lund T.C., Tolar J., De Meirleir K., Montoya J.G., Komaroff A.L., Ambros EE & Medveczky EG. (2010). - The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro. Proc. Natl Acad. Sci. USA, 107 (12), 5563-5568. doi:10.1073/pnas.0913586107.
Murakami Y., Minami M., Daimon Y. & Okanoue T. (2004). - Hepatitis B virus DNA in liver, serum, and peripheral blood mononuclear cells after the clearance of serum hepatitis B virus surface antigen. J. Med. Virol, 72 (2), 203-214. doi: 10.1002/ jmv.10547.
Stephen S.L., Sivanandam VG. & Kochanek S. (2008). -Homologous and heterologous recombination between adenovirus vector DNA and chromosomal DNA. J. Gene Med., 10 (11), 1176-1189. doi:10.1002/jgm, 1246.
Gallo R.C. (2015). - Developing a successful HIV vaccine. J. Inject. Dis., 212 (Suppl. 1), S40-S41. doi:10.1093/infdis/ jiv069.
Rodriguez S., Florins A., Gillet N., de Brogniez A., Sánchez-Alcaraz M.T., Boxus M., Boulanger E, Gutierrez G., Trono K., Alvarez I., Vagnoni L. & Willems L. (2011). - Freventive and therapeutic strategies for bovine leukemia virus: lessons for HTLV Viruses, 3 (7), 1210-1248. doi:10.3390/v3071210.
Kchour G., Rezaee R., Farid R., Ghantous A., Rafatpanah H., Tarhini M., Kooshyar M.M., El Hajj H., Berry E, Mortada M., Nasser R., Shirdel A., Dassouki Z., Ezzedine M., Rahimi H., Ghavamzadeh A., de The H., Hermine O., Mahmoudi M. & Bazarbachi A. (2013). - The combination of arsenic, interferon-alpha, and zidovudine restores an 'immunocompetent-like' cytokine expression profile in patients with adult T-cell leukemia lymphoma. Retrovirology, 10, 91. doi:10.1186/1742-4690-10-91.
Florins A., Gillet N., Asquith B., Boxus M., Burteau C., Twizere J.C., Urbain E, Vandermeers E, Debacq C, Sanchez-Alcaraz M.T., Schwartz-Cornil I., Kerkhofs E, Jean G., Thewis A., Hay J., Mortreux F., Wattel E., Reichert M., Bumy A., Kettmann R., BanghamC & WillemsL (2007).-Cell dynamics and immune response to BLV infection: a unifying model. Front. Biosci, 12, 1520-1531. doi: 10.2741/2165.
Lewis EE & Emerman M. (1994). - Passage through mitosis is required for oncoretroviruses but not for the human immunodeficiency virus. J. Virol., 68 (1), 510-516.
Roe T., Reynolds T.C., Yu G. & Brown P.O. (1993). -Integration of murine leukemia virus DNA depends on mitosis. EMBO J., 12(5), 2099-2108.
Suzuki Y. & Craigie R. (2007). - The road to chromatin -nuclear entry of retroviruses. Nat. Rev. Microbiol, 5 (3), 187-196. doi:10.1038/nrmicrol579.
Ao Z., Danappa Jayappa K., Wang B., Zheng Y, Kung S., Rassart E., Depping R., Kohler M., Cohen EA. & Yao X. (2010). - Importin alpha3 interacts with HIV-1 integrase and contributes to HIV-1 nuclear import and replication. J. Virol., 84 (17), 8650-8663. doi:10.1128/JVI.00508-10.
Christ F, Thys W, De Rijck J., Gijsbers R., Albanese A., Arosio D., Emiliani S., Rain J.C., Benarous R., Cereseto A. & Debyser Z. (2008). - Transportin-SR2 imports HIV into the nucleus. Curr. Biol, 18 (16), 1192-1202. doi: 10.1016/j. cub.2008.07.079.
Ciuffi A. (2008). - Mechanisms governing lentivirus integration site selection. Curr. Gene Ther., 8 (6), 419-429. doi:10.2174/156652308786848021.
Ciuffi A., Ronen K., Brady T., Malani N., Wang G, Berry C.C. & Bushman ED. (2009). - Methods for integration site distribution analyses in animal cell genomes. Methods, 47 (4), 261-268. doi:10.1016/j.ymeth.2008.10.028.
Bushman E, Lewinski M., Ciuffi A., Barr S., Leipzig J., Hannenhalli S. & Hoffmann C. (2005). - Genome-wide analysis of retroviral DNA integration. Nat. Rev. Microbiol, 3, 848-858. doi:10.1038/nrmicrol263.
Derse D., Crise B., Li Y., Princier G., Lum N., Stewart C, McGrath CF., Hughes S.H., Munroe D.J. & Wu X. (2007). - Human T-cell leukemia virus type 1 integration target sites in the human genome: comparison with those of other retroviruses. J. ViroL, 81 (12), 6731-6741. doi:10.1128/ JVI.02752-06.
Brady T, Roth ST., Malani N., Wang G.E, Berry C.C, Leboulch E, Hacein-Bey-Abina S., Cavazzana-Calvo M., Papapetrou E.P, Sadelain M., Savilahti H. & Bushman ED. (2011). - A method to sequence and quantify DNA integration for monitoring outcome in gene therapy. Nucleic Acids Res., 39 (11), e72. doi:10.1093/nar/gkrl40.
Roth S.L., Malani N. & Bushman ED.(2011).-Gammaretroviral integration into nucleosomal target DNA in vivo. J. ViroL, 85 (14), 7393-7401. doi:10.1128/JVI.00635-ll.
Mitchell R.S., Beitzel B.E, Schroder A.R., Shinn R, Chen H., Berry C.C, Ecker J.R. & Bushman ED. (2004). - Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol., 2, E234. doi:10.1371/journal. pbio.0020234.
Kim H.H., van den Heuvel A.P., Schmidt JW & Ross S.R. (2011). - Novel common integration sites targeted by mouse mammary tumor virus insertion in mammary tumors have oncogenic activity. PloS ONE, 6, e27425. doi:10.1371/journal. pone.0027425.
Brady T., Lee Y.N., Ronen K., Malani N., Berry C.C, Bieniasz ED. & Bushman ED. (2009). - Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev., 23, 633-642. doi:10.1101/gad. 1762309.
Wu X., Li Y., Crise B. & Burgess S.M. (2003). - Transcription start regions in the human genome are favored targets for MLV integration. Science, 300 (5626), 1749-1751. doi:10.1126/ science.1083413.
Gillet N.A., Gutierrez G., Rodriguez S.M, , de Brogniez A., Renotte N., Alvarez I., Trono K. & Willems L. (2013). -Massive depletion of bovine leukemia virus proviral clones located in genomic transcriptionally active sites during primary infection. PLoS Pathog., 9, e1003687. doi:10.1371/ journal.ppat. 1003687.
Faschinger A., Rouault E, Sollner J., Lukas A., Salmons B., Gunzburg WH. & Indik S. (2008). - Mouse mammary tumor virus integration site selection in human and mouse genomes. J. ViroL, 82 (3), 1360-1367. doi:10.1128/JVI.02098-07.
Wu X., Li Y, Crise B., Burgess S.M. & Munroe D.J. (2005). -Weak palindromic consensus sequences are a common feature found at the integration target sites of many retroviruses. J. ViroL, 79 (8), 5211-5214. doi:10.1128/JVI.79.8.5211-5214.2005.
Holman A.G & Coffin J.M. (2005). - Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites. Proc. Natl Acad. Sci. USA, 102 (17), 6103-6107. doi:10.1073/pnas.0501646102.
Desfarges S. & Ciuffi A. (2010). - Retroviral integration site selection. Viruses, 2 (1), 111-130. doi:10.3390/v2010111.
Roulston A., Marcellus R.C. & Branton RE. (1999). -Viruses and apoptosis. Annu. Rev. Microbiol., 53, 577-628. doi:10.1146/annurev.micro.53.1.577.
Kerkhofs R, Adam E., Droogmans L., Portetelle D., Mammerickx M., Burny A., Kettmann R. & Willems L. (1996). Cellular pathways involved in the ex vivo expression of bovine leukemia virus. J. Virol., 70 (4), 2170-2177.
Twizere J.C., Kruys V, Lefèbvre L, Vanderplasschen A., Colleté D., Debacq C, Lai W.S., Jauniaux J.C., Bernstein L, Semmes O.J., Burny A., Blackshear RJ., Kettmann R. & Willems L. (2003). - Interaction of retroviral tax oncoproteins with tristetraprolin and regulation of TNF- α expression. J. Natl Cancer Inst., 95 (24), 1846-1859. doi:10.1093/jnci/djgll8.
Witzany G. (2012). -Viruses: essential agents of life. Springer, Dordrecht, 428 pp. doi:10.1007/978-94-007-4899-6.
Arbuckle J.H. & Medveczky RG. (2011). - The molecular biology of human herpesvirus-6 latency and telomere integration. Microbes Infect., 13(8-9), 731-741. doi:10.1016/j. micinf.2011.03.006.
Achachi A., Florins A., Gillet N., Debacq C, Urbain P., Manfouo Foutsop G, Vandermeers F, Jasik A., Reichert M., Kerkhofs P., Lagneaux L., Burny A., Kettmann R. & Willems L. (2005). -Valproate activates bovine leukemia virus gene expression, triggers apoptosis and induces leukemia/ lymphoma regression in vivo. Proc. Natl Acad. Sci. USA, 102 (29), 10309-10314. doi:10.1073/pnas.0504248102.
Jaenisch R. (1976). - Germ line integration and Mendelian transmission of the exogenous Moloney leukemia virus. Proc. Natl Acad. Sci. USA, 73 (4), 1260-1264. doi:10.1073/ pnas.73.4.1260.
Blomberg J., Benachenhou E, Blikstad V, Sperber G. & Mayer J. (2009). - Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations. Gene, 448 (2), 115-123. doi:10.1016/j. gene.2009.06.007.
Jurka J., Kapitonov V.V. Pavlicek A., Klonowski R, Kohany O. & Walichiewicz J. (2005). - Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res., 110 (1-4), 462-467. doi:10.1159/000084979.
Goodier J.L. & Kazazian H.H. Jr (2008). - Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell, 135 (1), 23-35. doi:10.1016/j.cell.2008.09.022.
Jern R & Coffin J.M. (2008). - Effects of retroviruses on host genome function. Annu. Rev. Genet., 42, 709-732. doi:10.1146/annurev.genet.42.110807.091501.
Crochu S., Cook S., Attoui H., Charrel R.N., De Chesse R., Belhouchet M., Lemasson J.J., de Micco P. & de Lamballerie X. (2004). - Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes. J. Gen. Virol, 85 (7), 1971-1980. doi: 10.1099/vir.0.79850-0.
Horie M., Honda T., Suzuki Y., Kobayashi Y., Daito T., Oshida T., Ikuta K., Jern P., Gojobori T., Coffin J.M. & Tomonaga K. (2010). - Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature, 463, 84-87. doi:10.1038/nature08695.
Belyi VA., Levine AJ. & Skalka A.M. (2010). - Unexpected inheritance: multiple integrations of ancient Bornavirus and Ebolavfrus/Marburgvirus sequences in vertebrate genomes. PLoS Pathog., 6 (7), e1001030. doi:10.1371/journal. ppat.1001030.
Katzourakis A. & Gifford R.J. (2010). - Endogenous viral elements in animal genomes. PLoS Genet., 6 (11), e1001191. doi:10.1371/journal.pgen.l001191.
Kapoor A., Simmonds R & Lipkin WI. (2010). - Discovery and characterization of mammalian endogenous parvoviruses. J. Virol., 84 (24), 12628-12635. doi: 10.1128/JVI.01732-10.
Feng S., Jacobsen S.E. & Reik W (2010). - Epigenetic reprogramming in plant and animal development. Science, 330 (6004), 622-627. doi:10.1126/science,1190614.
Rawn S.M. & Cross J.C. (2008). - The evolution, regulation, and function of placenta-specific genes. Annu. Rev. Cell Dev. Biol, 24, 159-181. doi:10.1146/annurev cellbio.24.110707.175418.
Blaise S., de Parseval N., Benit L. & Heidmann T (2003). -Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc. Natl Acad. Sci. USA, 100 (22), 13013-13018. doi:10.1073/pnas.2132646100.
Dupressoir A., Vernochet C, Bawa O., Harper E, Pierron G., Opolon P. & Heidmann T (2009). - Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene. Proc. Natl Acad. Sci. USA, 106 (29), 12127-12132. doi:10.1073/ pnas.0902925106.
Klenerman R, Hengartner H. & Zinkernagel R.M. (1997). - A non-retroviral RNA virus persists in DNA form. Nature, 390, 298-301. doi: 10.1038/36876.
Geuking M.B., Weber J., Dewannieux M., Gorelik E., Heidmann T, Hengartner H, Zinkernagel R.M. & Hangartner L. (2009). - Recombination of retrotransposon and exogenous RNA virus results in nonretroviral cDNA integration. Science, 323 (5912), 393-396. doi:10.1126/ science. 1167375.
Hüser D., Gogol-Döring A., Lutter T., Weger S., Winter K., Hammer E.M., Cathomen T., Reinert K. & Heilbronn R. (2010). - Integration preferences of wildtype AAV-2 for consensus rep-binding sites at numerous loci in the human genome. PLoS Pathog., 6 (7), e1000985. doi:10.1371/journal. ppat.1000985.
Brister J.R. & Muzyczka N. (1999). - Rep-mediated nicking of the adeno-associated virus origin requires two biochemical activities, DNA helicase activity and transesterification. J. Virol, 73(11), 9325-9336.
McCarty D.M., Pereira D.J., Zolotukhin I., Zhou X., Ryan J.H. & Muzyczka N. (1994). - Identification of linear DNA sequences that specifically bind the adeno-associated virus Rep protein. J. Virol, 68 (8), 4988-4997.
Gao J., Luo X., Tang K., Li X. & Li G. (2006). - Epstein-Barr virus integrates frequently into chromosome 4q, 2q, lq and 7q of Burkitt's lymphoma cell line (Raji). J. Virol. Meth., 136 (1-2), 193-199. doi:10.1016/j.jviromet.2006.05.013.
Hurley E.A., Klaman L.D., Agger S., Lawrence J.B. & Thorley-Lawson DA. (1991). - The prototypical Epstein-Barr virus-transformed lymphoblastoid cell line IB4 is an unusual variant containing integrated but no episomal viral DNA. J. Virol, 65 (7), 3958-3963.
Lestou VS., De Braekeleer M., Strehl S., Ott G., Gadner H. & Ambros RE (1993). - Non-random integration of Epstein-Barr virus in lymphoblastoid cell lines. Genes Chromosomes Cancer, 8 (1), 38-48. doi:10.1002/gcc.2870080108.
Takakuwa T., Luo W.J., Ham M.E, Sakane-Ishikawa E, Wada N. & Aozasa K. (2004). - Integration of Epstein-Ban virus into chromosome 6ql5 of Burkitt lymphoma cell line (Raji) induces loss of BACH2 expression. Am. J. Pathol, 164 (3), 967-974. doi:10.1016/S0002-9440(10)63184-7.
Nacheva E.R, Ward K.N., Brazma D., Virgili A., Howard J., Leong H.N. & Clark DA. (2008). - Human herpesvirus 6 integrates within telomeric regions as evidenced by five different chromosomal sites. J. Med. Virol, 80 (11), 1952-1958. doi:10.1002/jmv.21299.
Neuveut C, Wei Y. & Buendia MA. (2010). - Mechanisms of HBV-related hepatocarcinogenesis. J. Hepatol, 52 (4), 594-604. doi: 10.1016/j.jhep.2009.10.033.
Murakami Y., Saigo K., Takashima H., Minami M., Okanoue T, Brechot C. & Paterlini-Brechot R (2005). - Large scaled analysis of hepatitis B virus (HBV) DNA integration in HBV related hepatocellular carcinomas. Gut, 54 (8), 1162-1168. doi: 10.1136/gut.2004.054452.
Tamori A., Nishiguchi S., Shiomi S., Hayashi T., Kobayashi S., Habu D., Takeda T., Seki S., Hirohashi K., Tanaka H. & Kubo S. (2005). - Hepatitis B virus DNA integration in hepatocellular carcinoma after interferon-induced disappearance of hepatitis C virus. Am.J. Gastroenterol, 100, 1748-1753. doi.10.1111/ j.1572-0241.2005.41914.x.
Ferber M.J., Montoya D.R, Yu C, Aderca 1., McGee A., Thorland E.C., Nagorney D.M., Gostout B.S., Burgart L.J., Boix L, Bruix J., McMahon B.J., Cheung T.H., Chung T.K., Wong Y.E, Smith D.I. & Roberts L.R. (2003). - Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers. Oncogene, 22, 3813-3820. doi:10.1038/sj.onc.l206528.
Stephen S.L., Montini E., Sivanandam VG., Al-Dhalimy M., Kestler H.A., Finegold M., Grompe M. & Kochanek S. (2010). - Chromosomal integration of adenoviral vector DNA in vivo. J. Virol., 84 (19), 9987-9994. doi:10.1128/JVI.00751-10
