Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination

• Published in: Retrovirology 2007-06, Vol.4 (1), p.39-39
• Main Authors: Flockerzi, Aline, Maydt, Jochen, Frank, Oliver, Ruggieri, Alessia, Maldener, Esther, Seifarth, Wolfgang, Medstrand, Patrik, Lengauer, Thomas, Meyerhans, Andreas, Leib-Mösch, Christine, Meese, Eckart, Mayer, Jens
• Format: Article
• Language: English
• Subjects: Base Sequence; Basic Medicine; DNA, Complementary - chemistry; DNA, Complementary - genetics; DNA, Complementary - isolation & purification; DNA, Viral - chemistry; DNA, Viral - genetics; DNA, Viral - isolation & purification; Endogenous Retroviruses - genetics; Farmakologi och toxikologi; Gene Expression; Genetic aspects; Genetic recombination; Genome, Human; Humans; Influence; Medical and Health Sciences; Medicin och hälsovetenskap; Medicinska och farmaceutiska grundvetenskaper; Molecular Sequence Data; Nucleotide sequence; Pharmacology and Toxicology; Phylogeny; Physiological aspects; Proviruses - genetics; Recombination, Genetic; Retroviruses; RNA, Viral - biosynthesis; RNA, Viral - genetics; Sequence Analysis, DNA; Sequence Homology; Software
• ISSN: 1742-4690; 1742-4690
• DOI: 10.1186/1742-4690-4-39

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. 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. 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.