Definition and variation of human endogenous retrovirus H.
We defined the abundant human endogenous retrovirus group HERV-H based on pol similarity. Among 3661 pol-containing elements, 1124 integrations were similar to HERV-H RGH2 pol using translated pol sequences. A clustering procedure lessened these to 234 representatives, amenable to detailed study. Among the 1124, 926 clustered into HERV-H and 106 into adjacent HERV-H-like, the remainder being more distant to HERV-H. The HERV-H group was divided into RTVLH2-like (705 elements) and RGH2-like (77 elements) subgroups. Among 926 HERV-H, LTR differences were 1-33%, 10% had env, 78% had gag, 66% had a histidine primer binding site (PBS), and 3% (both subgroups) had a phenylalanine PBS. Allelic differences in env were studied using a convenient temperature gradient gel electrophoresis (TGGE) method and a genomic single nucleotide polymorphism (SNP) search. A pattern of abundant defective elements and less abundant less defective ones led us to formulate a "midwife" master model where more complete elements help the others in trans to transpose.
Section of Virology, Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden. Patric.Jern@medsci.uu.se
Patric
P
Jern
Göran O
GO
Sperber
Jonas
J
Blomberg
D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D004251:DNA Transposable Elements; D004586:Electrophoresis / Q000379:methods; D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D015751:Genes, pol; D014644:Genetic Variation; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D013696:Temperature
D004251:DNA Transposable Elements