Abstract
Bovine leukemia virus (BLV) is an oncogenic retrovirus closely related to human T-cell lymphotropic virus. BLV-infected cattle are categorized as asymptomatic carriers or as having persistent lymphocytosis or enzootic bovine leukemia, depending on the clinical stage. We investigated the BLV integration site distribution at three BLV clinical stages and examined genome sequence features around the integration sites. In all, 264 BLV integration sites, at various locations on each chromosome, were identified in 28 cattle by inverse PCR and BLAST searches. Approximately one-third of BLV proviruses were independently integrated within transcriptional units, and approximately 10 % were integrated near transcription start sites. Moreover, less than 7 % of BLV integration sites were located near CpG islands. BLV did not preferentially integrate into transcriptionally active regions during any of the clinical stages. At the nucleotide level, regions around BLV integration points were significantly A/T rich with weak sequence consensus. BLV preferentially integrated within long interspersed nuclear repeat elements. Although BLV integration sites may not be associated with disease progression, integration is selective at the nucleotide level.
Similar content being viewed by others
References
Asfaw Y, Tsuduku S, Konishi M, Murakami K, Tsuboi T, Wu D, Sentsui H (2005) Distribution and superinfection of bovine leukemia virus genotypes in Japan. Arch Virol 150:493–505
Barr SD, Leipzig J, Shinn P, Ecker JR, Bushman FD (2005) Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome. J Virol 79:12035–12044
Bushman F, 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
Check E (2002) A tragic setback. Nature 420:116–118
Chou KS, Okayama A, Su IJ, Lee TH, Essex M (1996) Preferred nucleotide sequence at the integration target site of human T-cell leukemia virus type I from patients with adult T-cell leukemia. Int J Cancer 65:20–24
Ciuffi A, Llano M, Poeschla E, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman F (2005) A role for LEDGF/p75 in targeting HIV DNA integration. Nat Med 11:1287–1289
Couez D, Deschamps J, Kettmann R, Stephens RM, Gilden RV, Burny A (1984) Nucleotide sequence analysis of the long terminal repeat of integrated bovine leukemia provirus DNA and of adjacent viral and host sequences. J Virol 49:615–620
Crise B, Li Y, Yuan C, Morcock DR, Whitby D, Munroe DJ, Arthur LO, Wu X (2005) Simian immunodeficiency virus integration preference is similar to that of human immunodeficiency virus type 1. J Virol 79:12199–12204
Doi K, Wu X, Taniguchi Y, Yasunaga J, Satou Y, Okayama A, Nosaka K, Matsuoka M (2005) Preferential selection of human T-cell leukemia virus type I provirus integration sites in leukemic versus carrier states. Blood 106:1048–1053
Gillet N, Florins A, Boxus M, Burteau C, Nigro A, Vandermeers F, Balon H, Bouzar AB, Defoiche J, Burny A, Reichert M, Kettmann R, Willems L (2007) Mechanisms of leukemogenesis induced by bovine leukemia virus: prospects for novel anti-retroviral therapies in human. Retrovirology 4:18
Han Y, Lassen K, Monie D, Sedaghat AR, Shimoji S, Liu X, Pierson TC, Margolick JB, Siliciano RF, Siliciano JD (2004) Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. J Virol 78:6122–6133
Kattan T, MacNamara A, Rowan AG, Nose H, Mosley AJ, Tanaka Y, Taylor GP, Asquith B, Bangham CR (2009) The avidity and lytic efficiency of the CTL response to HTLV-1. J Immunol 182:5723–5729
Kettmann R, Meunier-Rotival M, Cortadas J, Cuny G, Ghysdael J, Mammerickx M, Burny A, Bernardi G (1979) Integration of bovine leukemia virus DNA in the bovine genome. Proc Natl Acad Sci USA 76:4822–4826
Kettmann R, Cleuter Y, Mammerickx M, Meunier-Rotival M, Bernardi G, Burny A, Chantrenne H (1980) Genomic integration of bovine leukemia provirus: comparison of persistent lymphocytosis with lymph node tumor form of enzootic. Proc Natl Acad Sci USA 77:2577–2581
Kettmann R, Deschamps J, Couez D, Claustriaux JJ, Palm R, Burny A (1983) Chromosome integration domain for bovine leukemia provirus in tumors. J Virol 47:146–150
Kiermer V, Van Lint C, Briclet D, Vanhulle C, Kettmann R, Verdin E, Burny A, Droogmans L (1998) An interferon regulatory factor binding site in the U5 region of the bovine leukemia virus long terminal repeat stimulates Tax-independent gene expression. J Virol 72:5526–5534
Leclercq I, Mortreux F, Cavrois M, Leroy A, Gessain A, Wain-Hobson S, Wattel E (2000) Host sequences flanking the human T-cell leukemia virus type 1 provirus in vivo. J Virol 74:2305–2312
Levy D, Deshayes L, Guillemain B, Parodi AL (1977) Bovine leukemia virus specific antibodies among French cattle. I. Comparison of complement fixation and hematological tests. Int J Cancer 19:822–827
Lewinski MK, Bushman FD (2005) Retroviral DNA integration–mechanism and consequences. Adv Genet 55:147–181
Llano M, Saenz DT, Meehan A, Wongthida P, Peretz M, Walker WH, Teo W, Poeschla EM (2006) An essential role for LEDGF/p75 in HIV integration. Science 314:461–464
Meekings KN, Leipzig J, Bushman FD, Taylor GP, Bangham CR (2008) HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP. PLoS Pathog 4:e1000027
Mirsky ML, Olmstead CA, Da Y, Lewin HA (1996) The prevalence of proviral bovine leukemia virus in peripheral blood mononuclear cells at two subclinical stages of infection. J Virol 70:2178–2183
Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry CC, Ecker JR, Bushman FD (2004) Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol 2:E234
Murakami H, Yamada T, Suzuki M, Nakahara Y, Suzuki K, Sentsui H (2011) Bovine leukemia virus integration site selection in cattle that develop leukemia. Virus Res 156:107–112
Murakami K, Kobayashi S, Konishi M, Kameyama K, Yamamoto T, Tsutsui T (2011) The recent prevalence of bovine leukemia virus (BLV) infection among Japanese cattle. Vet Microbiol 148:84–88
Narezkina A, Taganov KD, Litwin S, Stoyanova R, Hayashi J, Seeger C, Skalka AM, Katz RA (2004) Genome-wide analyses of avian sarcoma virus integration sites. J Virol 78:11656–11663
Rodriguez SM, Florins A, Gillet N, de Brogniez A, Sanchez-Alcaraz MT, Boxus M, Boulanger F, Gutierrez G, Trono K, Alvarez I, Vagnoni L, Willems L (2011) Preventive and therapeutic strategies for bovine leukemia virus: lessons for HTLV. Viruses 3:1210–1248
Sagata N, Yasunaga T, Ohishi K, Tsuzuku-Kawamura J, Onuma M, Ikawa Y (1984) Comparison of the entire genomes of bovine leukemia virus and human T-cell leukemia virus and characterization of their unidentified open reading frames. EMBO J 3:3231–3237
Schroder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F (2002) HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110:521–529
Team RDC (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Tsukahara T, Agawa H, Matsumoto S, Matsuda M, Ueno S, Yamashita Y, Yamada K, Tanaka N, Kojima K, Takeshita T (2006) Murine leukemia virus vector integration favors promoter regions and regional hot spots in a human T-cell line. Biochem Biophys Res Commun 345:1099–1107
Van der Maaten MJ, Miller JM (1976) Reprication of bovine leukemia virus in monolayer cell cultures. Bibl Haematol 43:360–362
Wu X, Li Y, Crise B, Burgess SM (2003) Transcription start regions in the human genome are favored targets for MLV integration. Science 300:1749–1751
Acknowledgement
We are grateful to members of the Tochigi Meat Inspection Station for helpful sampling. This work was supported by Grants-in-Aid for Science Research C (No. 22580357) from the Japan Society for the Promotion of Science, and the Academic Frontier Project for Private Universities from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Miyasaka, T., Oguma, K. & Sentsui, H. Distribution and characteristics of bovine leukemia virus integration sites in the host genome at three different clinical stages of infection. Arch Virol 160, 39–46 (2015). https://doi.org/10.1007/s00705-014-2224-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-014-2224-y