Definition and variation of human endogenous retrovirus H

Virology. 2004 Sep 15;327(1):93-110. doi: 10.1016/j.virol.2004.06.023.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Computational Biology
  • DNA Transposable Elements
  • Electrophoresis / methods
  • Endogenous Retroviruses / classification
  • Endogenous Retroviruses / genetics*
  • Evolution, Molecular
  • Genes, pol
  • Genetic Variation*
  • Humans
  • Molecular Sequence Data
  • Phylogeny
  • Polymerase Chain Reaction
  • Polymorphism, Single Nucleotide
  • Temperature

Substances

  • DNA Transposable Elements

Associated data

  • GENBANK/AY050297
  • GENBANK/AY050298