Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination.
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.
Flockerzi
Aline
A
Department of Human Genetics, Medical Faculty, University of Saarland, Homburg, Germany. aline.flockerzi@uniklinik-saarland.de
Maydt
Jochen
J
Frank
Oliver
O
Ruggieri
Alessia
A
Maldener
Esther
E
Seifarth
Wolfgang
W
Medstrand
Patrik
P
Lengauer
Thomas
T
Meyerhans
Andreas
A
Leib-Mösch
Christine
C
Meese
Eckart
E
Mayer
Jens
J
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
D018076:DNA, Complementary; D004279:DNA, Viral; D012367:RNA, Viral