title: Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination.
abstract: BACKGROUND
  The human genome comprises numerous human endogenous retroviruses (HERVs) that formed millions of years ago in ancestral species. A number of loci of the HERV-K(HML-2) family are evolutionarily much younger. A recent study suggested an infectious HERV-K(HML-2) variant in humans and other primates. Isolating such a variant from human individuals would be a significant finding for human biology.
  
  
  RESULTS
  When investigating expression patterns of specific HML-2 proviruses we encountered HERV-K(HML-2) cDNA sequences without proviral homologues in the human genome, named HERV-KX, that could very well support recently suggested infectious HML-2 variants. However, detailed sequence analysis, using the software RECCO, suggested that HERV-KX sequences were produced by recombination, possibly arising ex vivo, between transcripts from different HML-2 proviral loci.
  
  
  CONCLUSIONS
  As RT-PCR probably will be instrumental for isolating an infectious HERV-K(HML-2) variant, generation of "new" HERV-K(HML-2) sequences by ex vivo recombination seems inevitable. Further complicated by an unknown amount of allelic sequence variation in HERV-K(HML-2) proviruses, newly identified HERV-K(HML-2) variants should be interpreted very cautiously.
authors.affiliation: Department of Human Genetics, Medical Faculty, University of Saarland, Homburg, Germany. aline.flockerzi@uniklinik-saarland.de
authors.forename: Aline
authors.initials: A
authors.lastname: Flockerzi
authors.forename: Jochen
authors.initials: J
authors.lastname: Maydt
authors.forename: Oliver
authors.initials: O
authors.lastname: Frank
authors.forename: Alessia
authors.initials: A
authors.lastname: Ruggieri
authors.forename: Esther
authors.initials: E
authors.lastname: Maldener
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Seifarth
authors.forename: Patrik
authors.initials: P
authors.lastname: Medstrand
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
authors.forename: Andreas
authors.initials: A
authors.lastname: Meyerhans
authors.forename: Christine
authors.initials: C
authors.lastname: Leib-Mösch
authors.forename: Eckart
authors.initials: E
authors.lastname: Meese
authors.forename: Jens
authors.initials: J
authors.lastname: Mayer
mesh_terms: D001483:Base Sequence; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D020077:Endogenous Retroviruses / Q000235:genetics*; D015870:Gene Expression; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011533:Proviruses / Q000235:genetics; D012367:RNA, Viral / Q000096:biosynthesis* / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012984:Software
chemical_list: D018076:DNA, Complementary; D004279:DNA, Viral; D012367:RNA, Viral