A technique for genome-wide identification of differences in the interspersed repeats integrations between closely related genomes and its application to detection of human-specific integrations of HERV-K LTRs

TY - JOUR

T1 - A technique for genome-wide identification of differences in the interspersed repeats integrations between closely related genomes and its application to detection of human-specific integrations of HERV-K LTRs

AU - Buzdin, Anton

AU - Khodosevich, Konstantin

AU - Mamedov, Ilgar

AU - Vinogradova, Tatyana

AU - Lebedev, Yuri

AU - Hunsmann, Gerhard

AU - Sverdlov, Eugene

PY - 2002/3

Y1 - 2002/3

N2 - We have developed a method of targeted genomic difference analysis (TGDA) for genomewide detection of interspersed repeat integration site differences between closely related genomes. The method includes a whole-genome amplification of the flanks adjacent to target interspersed repetitive elements in both genomic DNAs under comparison, and subtractive hybridization (SH) of the selected amplicons. The potential of TGDA was demonstrated by the detection of differences in the integration sites of human endogenous retroviruses K (HERV-K) and related solitary long terminal repeats (LTRs) between the human and chimpanzee genomes. Of 55 randomly sequenced clones from a library enriched with human-specific integration (HSI) sites, 33 (60%) represented HSIs. All the human-specific (Hs) LTRs belong to two related evolutionarily young groups, suggesting simultaneous activity of two master genes in the hominid lineage. No deletion/insertion polymorphism was detected for the LTR HSIs for 25 unrelated caucasoid individuals. We also discuss the possible research applications for TGDA research.

AB - We have developed a method of targeted genomic difference analysis (TGDA) for genomewide detection of interspersed repeat integration site differences between closely related genomes. The method includes a whole-genome amplification of the flanks adjacent to target interspersed repetitive elements in both genomic DNAs under comparison, and subtractive hybridization (SH) of the selected amplicons. The potential of TGDA was demonstrated by the detection of differences in the integration sites of human endogenous retroviruses K (HERV-K) and related solitary long terminal repeats (LTRs) between the human and chimpanzee genomes. Of 55 randomly sequenced clones from a library enriched with human-specific integration (HSI) sites, 33 (60%) represented HSIs. All the human-specific (Hs) LTRs belong to two related evolutionarily young groups, suggesting simultaneous activity of two master genes in the hominid lineage. No deletion/insertion polymorphism was detected for the LTR HSIs for 25 unrelated caucasoid individuals. We also discuss the possible research applications for TGDA research.

KW - Animals

KW - Base Sequence

KW - Endogenous Retroviruses/genetics

KW - Genome, Human

KW - Humans

KW - Interspersed Repetitive Sequences/genetics

KW - Molecular Sequence Data

KW - Pan troglodytes/genetics

KW - Phylogeny

KW - Species Specificity

KW - Terminal Repeat Sequences/genetics

U2 - 10.1006/geno.2002.6705

DO - 10.1006/geno.2002.6705

M3 - Journal article

C2 - 11863371

SN - 0888-7543

VL - 79

SP - 413

EP - 422

JO - Genomics

JF - Genomics

IS - 3

ER -