DISTRIBUTION OF GENETIC POLYMORPHISMS IN HUMAN ENDOGENOUS RETRO VIRUSES AMONG VARIOUS ETHNIC POPULATIONS
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Date
2000-04
Department
Hood College Biology
Program
Biomedical and Environmental Science
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Abstract
Human endogenous retroviruses (HERVs) are defective proviruses
transmitted as stable Mendelian units vertically through the germline from one
generation to the next. This project compared classes I (ERV3) and II (HERV-K)
HERV env sequences among six divergent ethnic groups. Sequences related to
human T-cell lymphotropic virus type-1 (HTLV-1) were used as out-group
controls. Three novel single nucleotide polymorphisms (SNPs) were found in
ERV3, and one in HERV-K. Both novel and published polymorphisms were
screened on a panel of DNA representing six ethnic racial groups. SNPs tended
to be population specific and, for the most part, in Hardy-Weinberg equilibrium.
Primate DNA was sequenced at these polymorphic loci to determine sequence
homology in the human-primate lineage. Divergent nucleotides were found in
Class I (6.5%) and Class II (4.5%) HERVs. Phylogenetic analysis of ERV3 in the
primate lineage showed humans of Asian and Amer-Indian descent to be more
closely related than to other populations tested in this study.
This study also re-evaluated copy number in ERV3, a reportedly single
copy HERV. ERV3 was localized on chromosome 7 and Y by analysis of
somatic cell hybrids. Southern blot analysis indicated two copies on each
chromosome. Differences between copies on each hybrid were resolved by
sequence analysis. No difference in sequence was detected in either the LTRs
or env gene suggesting that the chromosome Y copy is a translocated copy from
chromosome 7 which may have occurred during the generation of somatic cell
hybrids.