FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Viruses / Characterization of Equine Infectious Anemia Virus Integrati...
Viruses2015; 7(6); 3241-3260; doi: 10.3390/v7062769

Characterization of Equine Infectious Anemia Virus Integration in the Horse Genome.

Abstract: Human immunodeficiency virus (HIV)-1 has a unique integration profile in the human genome relative to murine and avian retroviruses. Equine infectious anemia virus (EIAV) is another well-studied lentivirus that can also be used as a promising retro-transfection vector, but its integration into its native host has not been characterized. In this study, we mapped 477 integration sites of the EIAV strain EIAVFDDV13 in fetal equine dermal (FED) cells during in vitro infection. Published integration sites of EIAV and HIV-1 in the human genome were also analyzed as references. Our results demonstrated that EIAVFDDV13 tended to integrate into genes and AT-rich regions, and it avoided integrating into transcription start sites (TSS), which is consistent with EIAV and HIV-1 integration in the human genome. Notably, the integration of EIAVFDDV13 favored long interspersed elements (LINEs) and DNA transposons in the horse genome, whereas the integration of HIV-1 favored short interspersed elements (SINEs) in the human genome. The chromosomal environment near LINEs or DNA transposons potentially influences viral transcription and may be related to the unique EIAV latency states in equids. The data on EIAV integration in its natural host will facilitate studies on lentiviral infection and lentivirus-based therapeutic vectors.
Get Full Text
Publication Date: 2015-06-19 PubMed ID: 26102582PubMed Central: PMC4488736DOI: 10.3390/v7062769Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Comparative Study
  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses an in-depth study of the integration of Equine Infectious Anemia Virus (EIAV) in the genome of a horse. The study uses EIAV strain EIAVFDDV13 and investigates its tendency to integrate into certain sections of the horse genome, shedding light on its behavior and potential for use as a retro-transfection vector.

Research Methodology

  • An in vitro infection is conducted using the EIAV strain known as EIAVFDDV13. The fetal equine dermal (FED) cells are the primary subjects for this experiment.
  • Integration points of EIAVFDDV13 in the horse genome are traced, with a total of 477 integration sites being mapped in the FED cells.
  • For comparison reasons, earlier published integration sites of EIAV and HIV-1 in the human genome are taken into consideration.

Findings and Observations

  • The research reveals that EIAVFDDV13 tends to integrate into genes, primarily leaning towards the AT-rich regions.
  • Further, the integration avoids transcription start sites (TSS), which marries with the behavior of EIAV and HIV-1 when they integrate into the human genome.
  • One significant observation that differentiates EIAV from HIV-1 is that EIAV favors integration in long interspersed elements (LINEs) and DNA transposons within the horse genome. In contrast, HIV-1 opts for short interspersed elements (SINEs) within the human genome.

Conclusion and Implications

  • The chromosomal environment around LINEs or DNA transposons could potentially affect viral transcription. This has implications for the distinct EIAV latency states in equids.
  • The findings present the behavior of EIAV in its natural host, providing considerable aid to research on lentiviral infections and the development of therapeutic lentivirus-based vectors.

Cite This Article

APA
Liu Q, Wang XF, Ma J, He XJ, Wang XJ, Zhou JH. (2015). Characterization of Equine Infectious Anemia Virus Integration in the Horse Genome. Viruses, 7(6), 3241-3260. https://doi.org/10.3390/v7062769

Publication

Viruses
ISSN: 1999-4915
NlmUniqueID: 101509722
Country: Switzerland
Language: English
Volume: 7
Issue: 6
Pages: 3241-3260

Researcher Affiliations

Liu, Qiang
  • State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China. liuqiang_yyy@163.com.
Wang, Xue-Feng
  • State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China. xuefengwang1982@126.com.
Ma, Jian
  • State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China. jma@hvri.ac.cn.
He, Xi-Jun
  • State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China. hexijun@caas.cn.
Wang, Xiao-Jun
  • State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China. xjw@hvri.ac.cn.
Zhou, Jian-Hua
  • State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China. jianhua_uc@126.com.

MeSH Terms

  • Animals
  • Cells, Cultured
  • Chromosomes / virology
  • DNA, Viral / analysis
  • DNA, Viral / genetics
  • Epithelial Cells / virology
  • Genetic Loci
  • Genome
  • HIV-1 / genetics
  • HIV-1 / physiology
  • Horses
  • Humans
  • Infectious Anemia Virus, Equine / genetics
  • Infectious Anemia Virus, Equine / physiology
  • Proviruses / genetics
  • Virus Integration

References

This article includes 68 references
  1. Coffin JM, Hughes SH, Varmus HE. The Interactions of Retroviruses and their Hosts. In: Coffin J.M., Hughes S.H., Varmus H.E., editors. Retroviruses. Cold Spring Harbor; New York, NY, USA: 1997.
  2. Van Maele B, Debyser Z. HIV-1 integration: an interplay between HIV-1 integrase, cellular and viral proteins.. AIDS Rev 2005 Jan-Mar;7(1):26-43.
    pubmed: 15875659
  3. Debyser Z, Christ F, De Rijck J, Gijsbers R. Host factors for retroviral integration site selection.. Trends Biochem Sci 2015 Feb;40(2):108-16.
    doi: 10.1016/j.tibs.2014.12.001pubmed: 25555456google scholar: lookup
  4. Biasco L, Baricordi C, Aiuti A. Retroviral integrations in gene therapy trials.. Mol Ther 2012 Apr;20(4):709-16.
    doi: 10.1038/mt.2011.289pmc: PMC3321603pubmed: 22252453google scholar: lookup
  5. Boztug K, Dewey RA, Klein C. Development of hematopoietic stem cell gene therapy for Wiskott-Aldrich syndrome.. Curr Opin Mol Ther 2006 Oct;8(5):390-5.
    pubmed: 17078381
  6. Fischer A, Hacein-Bey-Abina S, Cavazzana-Calvo M. Gene therapy for primary adaptive immune deficiencies.. J Allergy Clin Immunol 2011 Jun;127(6):1356-9.
    doi: 10.1016/j.jaci.2011.04.030pubmed: 21624615google scholar: lookup
  7. Rivat C, Santilli G, Gaspar HB, Thrasher AJ. Gene therapy for primary immunodeficiencies.. Hum Gene Ther 2012 Jul;23(7):668-75.
    doi: 10.1089/hum.2012.116pmc: PMC3404418pubmed: 22691036google scholar: lookup
  8. Verma IM, Weitzman MD. Gene therapy: twenty-first century medicine.. Annu Rev Biochem 2005;74:711-38.
    doi: 10.1146/annurev.biochem.74.050304.091637pubmed: 15952901google scholar: lookup
  9. Pike-Overzet K, van der Burg M, Wagemaker G, van Dongen JJ, Staal FJ. New insights and unresolved issues regarding insertional mutagenesis in X-linked SCID gene therapy.. Mol Ther 2007 Nov;15(11):1910-6.
    doi: 10.1038/sj.mt.6300297pubmed: 17726455google scholar: lookup
  10. Cavazzana-Calvo M, Fischer A. Gene therapy for severe combined immunodeficiency: are we there yet?. J Clin Invest 2007 Jun;117(6):1456-65.
    doi: 10.1172/JCI30953pmc: PMC1878528pubmed: 17549248google scholar: lookup
  11. Voigt K, Izsvák Z, Ivics Z. Targeted gene insertion for molecular medicine.. J Mol Med (Berl) 2008 Nov;86(11):1205-19.
    doi: 10.1007/s00109-008-0381-8pubmed: 18607557google scholar: lookup
  12. Hacein-Bey-Abina S, Von Kalle C, Schmidt M, McCormack MP, Wulffraat N, Leboulch P, Lim A, Osborne CS, Pawliuk R, Morillon E, Sorensen R, Forster A, Fraser P, Cohen JI, de Saint Basile G, Alexander I, Wintergerst U, Frebourg T, Aurias A, Stoppa-Lyonnet D, Romana S, Radford-Weiss I, Gross F, Valensi F, Delabesse E, Macintyre E, Sigaux F, Soulier J, Leiva LE, Wissler M, Prinz C, Rabbitts TH, Le Deist F, Fischer A, Cavazzana-Calvo M. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1.. Science 2003 Oct 17;302(5644):415-9.
    doi: 10.1126/science.1088547pubmed: 14564000google scholar: lookup
  13. Hacein-Bey-Abina S, Garrigue A, Wang GP, Soulier J, Lim A, Morillon E, Clappier E, Caccavelli L, Delabesse E, Beldjord K, Asnafi V, MacIntyre E, Dal Cortivo L, Radford I, Brousse N, Sigaux F, Moshous D, Hauer J, Borkhardt A, Belohradsky BH, Wintergerst U, Velez MC, Leiva L, Sorensen R, Wulffraat N, Blanche S, Bushman FD, Fischer A, Cavazzana-Calvo M. Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1.. J Clin Invest 2008 Sep;118(9):3132-42.
    doi: 10.1172/JCI35700pmc: PMC2496963pubmed: 18688285google scholar: lookup
  14. Hacein-Bey-Abina S, von Kalle C, Schmidt M, Le Deist F, Wulffraat N, McIntyre E, Radford I, Villeval JL, Fraser CC, Cavazzana-Calvo M, Fischer A. A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency.. N Engl J Med 2003 Jan 16;348(3):255-6.
    doi: 10.1056/NEJM200301163480314pubmed: 12529469google scholar: lookup
  15. Wang GP, Garrigue A, Ciuffi A, Ronen K, Leipzig J, Berry C, Lagresle-Peyrou C, Benjelloun F, Hacein-Bey-Abina S, Fischer A, Cavazzana-Calvo M, Bushman FD. DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer.. Nucleic Acids Res 2008 May;36(9):e49.
    doi: 10.1093/nar/gkn125pmc: PMC2396413pubmed: 18411205google scholar: lookup
  16. Wang GP, Levine BL, Binder GK, Berry CC, Malani N, McGarrity G, Tebas P, June CH, Bushman FD. Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells.. Mol Ther 2009 May;17(5):844-50.
    doi: 10.1038/mt.2009.16pmc: PMC2835137pubmed: 19259065google scholar: lookup
  17. Montini E, Cesana D, Schmidt M, Sanvito F, Bartholomae CC, Ranzani M, Benedicenti F, Sergi LS, Ambrosi A, Ponzoni M, Doglioni C, Di Serio C, von Kalle C, Naldini L. The genotoxic potential of retroviral vectors is strongly modulated by vector design and integration site selection in a mouse model of HSC gene therapy.. J Clin Invest 2009 Apr;119(4):964-75.
    doi: 10.1172/JCI37630pmc: PMC2662564pubmed: 19307726google scholar: lookup
  18. Papayannakos C, Daniel R. Understanding lentiviral vector chromatin targeting: working to reduce insertional mutagenic potential for gene therapy.. Gene Ther 2013 Jun;20(6):581-8.
    doi: 10.1038/gt.2012.88pubmed: 23171920google scholar: lookup
  19. Schröder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots.. Cell 2002 Aug 23;110(4):521-9.
    doi: 10.1016/S0092-8674(02)00864-4pubmed: 12202041google scholar: lookup
  20. Crise B, Li Y, Yuan C, Morcock DR, Whitby D, Munroe DJ, Arthur LO, Wu X. Simian immunodeficiency virus integration preference is similar to that of human immunodeficiency virus type 1.. J Virol 2005 Oct;79(19):12199-204.
    doi: 10.1128/JVI.79.19.12199-12204.2005pmc: PMC1211548pubmed: 16160146google scholar: lookup
  21. Kang Y, Moressi CJ, Scheetz TE, Xie L, Tran DT, Casavant TL, Ak P, Benham CJ, Davidson BL, McCray PB Jr. Integration site choice of a feline immunodeficiency virus vector.. J Virol 2006 Sep;80(17):8820-3.
    doi: 10.1128/JVI.00719-06pmc: PMC1563849pubmed: 16912328google scholar: lookup
  22. Wu X, Li Y, Crise B, Burgess SM. Transcription start regions in the human genome are favored targets for MLV integration.. Science 2003 Jun 13;300(5626):1749-51.
    doi: 10.1126/science.1083413pubmed: 12805549google scholar: lookup
  23. Narezkina A, Taganov KD, Litwin S, Stoyanova R, Hayashi J, Seeger C, Skalka AM, Katz RA. Genome-wide analyses of avian sarcoma virus integration sites.. J Virol 2004 Nov;78(21):11656-63.
    doi: 10.1128/JVI.78.21.11656-11663.2004pmc: PMC523270pubmed: 15479807google scholar: lookup
  24. Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences.. PLoS Biol 2004 Aug;2(8):E234.
    doi: 10.1371/journal.pbio.0020234pmc: PMC509299pubmed: 15314653google scholar: lookup
  25. Craigo JK, Montelaro RC. Lessons in AIDS vaccine development learned from studies of equine infectious, anemia virus infection and immunity.. Viruses 2013 Dec 2;5(12):2963-76.
    doi: 10.3390/v5122963pmc: PMC3967156pubmed: 24316675google scholar: lookup
  26. Leroux C, Cadoré JL, Montelaro RC. Equine Infectious Anemia Virus (EIAV): what has HIV's country cousin got to tell us?. Vet Res 2004 Jul-Aug;35(4):485-512.
    doi: 10.1051/vetres:2004020pubmed: 15236678google scholar: lookup
  27. Harrold SM, Cook SJ, Cook RF, Rushlow KE, Issel CJ, Montelaro RC. Tissue sites of persistent infection and active replication of equine infectious anemia virus during acute disease and asymptomatic infection in experimentally infected equids.. J Virol 2000 Apr;74(7):3112-21.
    doi: 10.1128/JVI.74.7.3112-3121.2000pmc: PMC111810pubmed: 10708426google scholar: lookup
  28. Kono Y, Hirasawa K, Fukunaga Y, Taniguchi T. Recrudescence of equine infectious anemia by treatment with immunosuppressive drugs.. Natl Inst Anim Health Q (Tokyo) 1976 Spring;16(1):8-15.
    pubmed: 177894
  29. Craigo JK, Leroux C, Howe L, Steckbeck JD, Cook SJ, Issel CJ, Montelaro RC. Transient immune suppression of inapparent carriers infected with a principal neutralizing domain-deficient equine infectious anaemia virus induces neutralizing antibodies and lowers steady-state virus replication.. J Gen Virol 2002 Jun;83(Pt 6):1353-1359.
    pubmed: 12029150doi: 10.1099/0022-1317-83-6-1353google scholar: lookup
  30. Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription.. J Virol 2005 Jun;79(11):6610-9.
    doi: 10.1128/JVI.79.11.6610-6619.2005pmc: PMC1112149pubmed: 15890899google scholar: lookup
  31. Pace MJ, Graf EH, Agosto LM, Mexas AM, Male F, Brady T, Bushman FD, O'Doherty U. Directly infected resting CD4+T cells can produce HIV Gag without spreading infection in a model of HIV latency.. PLoS Pathog 2012;8(7):e1002818.
    doi: 10.1371/journal.ppat.1002818pmc: PMC3406090pubmed: 22911005google scholar: lookup
  32. Han Y, Lassen K, Monie D, Sedaghat AR, Shimoji S, Liu X, Pierson TC, Margolick JB, Siliciano RF, Siliciano JD. 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 2004 Jun;78(12):6122-33.
    doi: 10.1128/JVI.78.12.6122-6133.2004pmc: PMC416493pubmed: 15163705google scholar: lookup
  33. Hacker CV, Vink CA, Wardell TW, Lee S, Treasure P, Kingsman SM, Mitrophanous KA, Miskin JE. The integration profile of EIAV-based vectors.. Mol Ther 2006 Oct;14(4):536-45.
    doi: 10.1016/j.ymthe.2006.06.006pubmed: 16950499google scholar: lookup
  34. Marshall HM, Ronen K, Berry C, Llano M, Sutherland H, Saenz D, Bickmore W, Poeschla E, Bushman FD. Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting.. PLoS One 2007 Dec 19;2(12):e1340.
    doi: 10.1371/journal.pone.0001340pmc: PMC2129110pubmed: 18092005google scholar: lookup
  35. Ma J, Shi N, Jiang CG, Lin YZ, Wang XF, Wang S, Lv XL, Zhao LP, Shao YM, Kong XG, Zhou JH, Shen RX. A proviral derivative from a reference attenuated EIAV vaccine strain failed to elicit protective immunity.. Virology 2011 Feb 5;410(1):96-106.
    doi: 10.1016/j.virol.2010.10.032pubmed: 21094511google scholar: lookup
  36. Ma J, Wang SS, Lin YZ, Liu HF, Wei HM, Du C, Wang XF, Zhou JH. An attenuated EIAV strain and its molecular clone strain differentially induce the expression of Toll-like receptors and type-I interferons in equine monocyte-derived macrophages.. Vet Microbiol 2013 Sep 27;166(1-2):263-9.
    doi: 10.1016/j.vetmic.2013.06.005pubmed: 23850441google scholar: lookup
  37. Qi X, Wang X, Wang S, Lin Y, Jiang C, Ma J, Zhao L, Lv X, Shen R, Wang F, Kong X, Su Z, Zhou J. Genomic analysis of an effective lentiviral vaccine-attenuated equine infectious anemia virus vaccine EIAV FDDV13.. Virus Genes 2010 Aug;41(1):86-98.
    doi: 10.1007/s11262-010-0491-6pubmed: 20526660google scholar: lookup
  38. Huang J, Zhao Y, Shiraigol W, Li B, Bai D, Ye W, Daidiikhuu D, Yang L, Jin B, Zhao Q, Gao Y, Wu J, Bao W, Li A, Zhang Y, Han H, Bai H, Bao Y, Zhao L, Zhai Z, Zhao W, Sun Z, Zhang Y, Meng H, Dugarjaviin M. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.. Sci Rep 2014 May 14;4:4958.
    doi: 10.1038/srep04958pmc: PMC4021364pubmed: 24828444google scholar: lookup
  39. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
    doi: 10.1126/science.1178158pmc: PMC3785132pubmed: 19892987google scholar: lookup
  40. Jiang CG, Gao X, Ma J, Lin YZ, Wang XF, Zhao LP, Hua YP, Liu D, Zhou JH. C-terminal truncation of the transmembrane protein of an attenuated lentiviral vaccine alters its in vitro but not in vivo replication and weakens its potential pathogenicity.. Virus Res 2011 Jun;158(1-2):235-45.
    doi: 10.1016/j.virusres.2011.04.007pubmed: 21539871google scholar: lookup
  41. Morrow CD, Park J, Wakefield JK. Viral gene products and replication of the human immunodeficiency type 1 virus.. Am J Physiol 1994 May;266(5 Pt 1):C1135-56.
    pubmed: 8203479doi: 10.1152/ajpcell.1994.266.5.c1135google scholar: lookup
  42. Ranki A, Lagerstedt A, Ovod V, Aavik E, Krohn KJ. Expression kinetics and subcellular localization of HIV-1 regulatory proteins Nef, Tat and Rev in acutely and chronically infected lymphoid cell lines.. Arch Virol 1994;139(3-4):365-78.
    doi: 10.1007/BF01310798pubmed: 7832642google scholar: lookup
  43. Ciuffi A, Ronen K, Brady T, Malani N, Wang G, Berry CC, Bushman FD. Methods for integration site distribution analyses in animal cell genomes.. Methods 2009 Apr;47(4):261-8.
    doi: 10.1016/j.ymeth.2008.10.028pmc: PMC4104535pubmed: 19038346google scholar: lookup
  44. Ciuffi A, Barr SD. Identification of HIV integration sites in infected host genomic DNA.. Methods 2011 Jan;53(1):39-46.
    doi: 10.1016/j.ymeth.2010.04.004pubmed: 20385239google scholar: lookup
  45. Holman AG, Coffin JM. Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites.. Proc Natl Acad Sci U S A 2005 Apr 26;102(17):6103-7.
    doi: 10.1073/pnas.0501646102pmc: PMC1087937pubmed: 15802467google scholar: lookup
  46. Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications.. Genome Res 2007 Aug;17(8):1186-94.
    doi: 10.1101/gr.6286907pmc: PMC1933515pubmed: 17545577google scholar: lookup
  47. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Deslattes Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. The sequence of the human genome.. Science 2001 Feb 16;291(5507):1304-51.
    doi: 10.1126/science.1058040pubmed: 11181995google scholar: lookup
  48. Berry C, Hannenhalli S, Leipzig J, Bushman FD. Selection of target sites for mobile DNA integration in the human genome.. PLoS Comput Biol 2006 Nov 24;2(11):e157.
    doi: 10.1371/journal.pcbi.0020157pmc: PMC1664696pubmed: 17166054google scholar: lookup
  49. Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH. HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells.. Science 2014 Jul 11;345(6193):179-83.
    doi: 10.1126/science.1254194pmc: PMC4262401pubmed: 24968937google scholar: lookup
  50. Shan L, Yang HC, Rabi SA, Bravo HC, Shroff NS, Irizarry RA, Zhang H, Margolick JB, Siliciano JD, Siliciano RF. Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model.. J Virol 2011 Jun;85(11):5384-93.
    doi: 10.1128/JVI.02536-10pmc: PMC3094997pubmed: 21430059google scholar: lookup
  51. Cohn LB, Silva IT, Oliveira TY, Rosales RA, Parrish EH, Learn GH, Hahn BH, Czartoski JL, McElrath MJ, Lehmann C, Klein F, Caskey M, Walker BD, Siliciano JD, Siliciano RF, Jankovic M, Nussenzweig MC. HIV-1 integration landscape during latent and active infection.. Cell 2015 Jan 29;160(3):420-32.
    doi: 10.1016/j.cell.2015.01.020pmc: PMC4371550pubmed: 25635456google scholar: lookup
  52. Sherrill-Mix S, Lewinski MK, Famiglietti M, Bosque A, Malani N, Ocwieja KE, Berry CC, Looney D, Shan L, Agosto LM, Pace MJ, Siliciano RF, O'Doherty U, Guatelli J, Planelles V, Bushman FD. HIV latency and integration site placement in five cell-based models.. Retrovirology 2013 Aug 16;10:90.
    doi: 10.1186/1742-4690-10-90pmc: PMC3765678pubmed: 23953889google scholar: lookup
  53. Ciuffi A, Mohammadi P, Golumbeanu M, di Iulio J, Telenti A. Bioinformatics and HIV latency.. Curr HIV/AIDS Rep 2015 Mar;12(1):97-106.
    doi: 10.1007/s11904-014-0240-xpmc: PMC4369283pubmed: 25586146google scholar: lookup
  54. Desfarges S, Ciuffi A. Retroviral integration site selection.. Viruses 2010 Jan;2(1):111-130.
    doi: 10.3390/v2010111pmc: PMC3185549pubmed: 21994603google scholar: lookup
  55. De Ravin SS, Su L, Theobald N, Choi U, Macpherson JL, Poidinger M, Symonds G, Pond SM, Ferris AL, Hughes SH, Malech HL, Wu X. Enhancers are major targets for murine leukemia virus vector integration.. J Virol 2014 Apr;88(8):4504-13.
    doi: 10.1128/JVI.00011-14pmc: PMC3993722pubmed: 24501411google scholar: lookup
  56. Tsukahara T, Agawa H, Matsumoto S, Matsuda M, Ueno S, Yamashita Y, Yamada K, Tanaka N, Kojima K, Takeshita T. Murine leukemia virus vector integration favors promoter regions and regional hot spots in a human T-cell line.. Biochem Biophys Res Commun 2006 Jul 7;345(3):1099-107.
    doi: 10.1016/j.bbrc.2006.05.007pubmed: 16713998google scholar: lookup
  57. Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: viral and cellular determinants of target-site selection.. PLoS Pathog 2006 Jun;2(6):e60.
    doi: 10.1371/journal.ppat.0020060pmc: PMC1480600pubmed: 16789841google scholar: lookup
  58. Kvaratskhelia M, Sharma A, Larue RC, Serrao E, Engelman A. Molecular mechanisms of retroviral integration site selection.. Nucleic Acids Res 2014;42(16):10209-25.
    doi: 10.1093/nar/gku769pmc: PMC4176367pubmed: 25147212google scholar: lookup
  59. Busschots K, Vercammen J, Emiliani S, Benarous R, Engelborghs Y, Christ F, Debyser Z. The interaction of LEDGF/p75 with integrase is lentivirus-specific and promotes DNA binding.. J Biol Chem 2005 May 6;280(18):17841-7.
    doi: 10.1074/jbc.M411681200pubmed: 15749713google scholar: lookup
  60. Cherepanov P. LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro.. Nucleic Acids Res 2007;35(1):113-24.
    doi: 10.1093/nar/gkl885pmc: PMC1802576pubmed: 17158150google scholar: lookup
  61. Schaller T, Ocwieja KE, Rasaiyaah J, Price AJ, Brady TL, Roth SL, Hué S, Fletcher AJ, Lee K, KewalRamani VN, Noursadeghi M, Jenner RG, James LC, Bushman FD, Towers GJ. HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency.. PLoS Pathog 2011 Dec;7(12):e1002439.
    doi: 10.1371/journal.ppat.1002439pmc: PMC3234246pubmed: 22174692google scholar: lookup
  62. De Rijck J, de Kogel C, Demeulemeester J, Vets S, El Ashkar S, Malani N, Bushman FD, Landuyt B, Husson SJ, Busschots K, Gijsbers R, Debyser Z. The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites.. Cell Rep 2013 Nov 27;5(4):886-94.
    doi: 10.1016/j.celrep.2013.09.040pmc: PMC4197836pubmed: 24183673google scholar: lookup
  63. Gupta SS, Maetzig T, Maertens GN, Sharif A, Rothe M, Weidner-Glunde M, Galla M, Schambach A, Cherepanov P, Schulz TF. Bromo- and extraterminal domain chromatin regulators serve as cofactors for murine leukemia virus integration.. J Virol 2013 Dec;87(23):12721-36.
    doi: 10.1128/JVI.01942-13pmc: PMC3838128pubmed: 24049186google scholar: lookup
  64. Sharma A, Larue RC, Plumb MR, Malani N, Male F, Slaughter A, Kessl JJ, Shkriabai N, Coward E, Aiyer SS, Green PL, Wu L, Roth MJ, Bushman FD, Kvaratskhelia M. BET proteins promote efficient murine leukemia virus integration at transcription start sites.. Proc Natl Acad Sci U S A 2013 Jul 16;110(29):12036-41.
    doi: 10.1073/pnas.1307157110pmc: PMC3718171pubmed: 23818621google scholar: lookup
  65. Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes.. Curr Opin Genet Dev 1999 Dec;9(6):657-63.
    doi: 10.1016/S0959-437X(99)00031-3pubmed: 10607616google scholar: lookup
  66. Han JS, Szak ST, Boeke JD. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes.. Nature 2004 May 20;429(6989):268-74.
    doi: 10.1038/nature02536pubmed: 15152245google scholar: lookup
  67. Muñoz-López M, García-Pérez JL. DNA transposons: nature and applications in genomics.. Curr Genomics 2010 Apr;11(2):115-28.
    doi: 10.2174/138920210790886871pmc: PMC2874221pubmed: 20885819google scholar: lookup
  68. Yant SR, Wu X, Huang Y, Garrison B, Burgess SM, Kay MA. High-resolution genome-wide mapping of transposon integration in mammals.. Mol Cell Biol 2005 Mar;25(6):2085-94.
    doi: 10.1128/MCB.25.6.2085-2094.2005pmc: PMC1061620pubmed: 15743807google scholar: lookup

Citations

This article has been cited 0 times.
Subscribe to our newsletter
Join 99,344 horse owners like you who receive our email updates on horse health and nutrition.