title: Genome-wide mapping of foamy virus vector integrations into a human cell line.
abstract: Integration-site selection by retroviruses and retroviral vectors has gained increased scientific interest. Foamy viruses (FVs) constitute a unique subfamily (Spumavirinae) of the family Retroviridae, for which the integration pattern into the human genome has not yet been determined. To accomplish this, 293 cells were transduced with FV vectors and the integration sites into the cellular genome were determined by a high-throughput method based on inverse PCR. For comparison, a limited number of murine leukemia virus (MLV) and human immunodeficiency virus (HIV) integration sites were analysed in parallel. Altogether, 628 FV, 87 HIV and 141 MLV distinct integration sites were mapped to the human genome. The sequences were analysed for RefSeq genes, promoter regions, CpG islands and insertions into cellular oncogenes. Compared with the integration-site preferences of HIV, which strongly favours active genes, and MLV, which favours integration near transcription-start regions, our results indicate that FV integration has neither of these preferences. However, once integration has occurred into a transcribed region of the genome, FVs tend to target promoter-close regions, albeit with less preference than MLV. Furthermore, our study revealed a palindromic consensus sequence for integration, which was centred on the virus-specific, four-base-duplicated target site. In summary, it is shown that the integration pattern of FVs appears to be unique compared with those of other retroviral genera.
authors.affiliation: Institut für Virologie und Immunbiologie, Universität Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
authors.forename: Ali
authors.initials: A
authors.lastname: Nowrouzi
authors.affiliation: Lehrstuhl für Bioinformatik, Universität Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Dittrich
authors.affiliation: Division of Experimental Hematology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, USA.
authors.forename: Chuck
authors.initials: C
authors.lastname: Klanke
authors.affiliation: Institut für Virologie und Immunbiologie, Universität Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Heinkelein
authors.affiliation: Institut für Virologie und Immunbiologie, Universität Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Rammling
authors.affiliation: Lehrstuhl für Bioinformatik, Universität Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.affiliation: Division of Experimental Hematology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, USA.
authors.forename: Christof
authors.initials: C
authors.lastname: von Kalle
authors.affiliation: Institut für Virologie und Immunbiologie, Universität Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
authors.forename: Axel
authors.initials: A
authors.lastname: Rethwilm
mesh_terms: D002460:Cell Line; D016678:Genome / Q000235:genetics; D006801:Humans; D007668:Kidney; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D016092:Spumavirus / Q000502:physiology*; D016662:Virus Integration