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

Anton Buzdin; Konstantin Khodosevich; Ilgar Mamedov; Tatyana Vinogradova; Yuri Lebedev; Gerhard Hunsmann; Eugene Sverdlov

doi:10.1006/geno.2002.6705

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

Anton Buzdin, Konstantin Khodosevich, Ilgar Mamedov, Tatyana Vinogradova, Yuri Lebedev, Gerhard Hunsmann, Eugene Sverdlov

38 Citations (Scopus)

Abstract

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.

Original language	English
Journal	Genomics
Volume	79
Issue number	3
Pages (from-to)	413-22
Number of pages	10
ISSN	0888-7543
DOIs	https://doi.org/10.1006/geno.2002.6705
Publication status	Published - Mar 2002
Externally published	Yes

Keywords

Animals
Base Sequence
Endogenous Retroviruses/genetics
Genome, Human
Humans
Interspersed Repetitive Sequences/genetics
Molecular Sequence Data
Pan troglodytes/genetics
Phylogeny
Species Specificity
Terminal Repeat Sequences/genetics

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10.1006/geno.2002.6705

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Buzdin, A., Khodosevich, K., Mamedov, I., Vinogradova, T., Lebedev, Y., Hunsmann, G., & Sverdlov, E. (2002). 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. Genomics, 79(3), 413-22. https://doi.org/10.1006/geno.2002.6705

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. / Buzdin, Anton; Khodosevich, Konstantin; Mamedov, Ilgar et al.
In: Genomics, Vol. 79, No. 3, 03.2002, p. 413-22.

Research output: Contribution to journal › Journal article › Research › peer-review

Buzdin, A, Khodosevich, K, Mamedov, I, Vinogradova, T, Lebedev, Y, Hunsmann, G & Sverdlov, E 2002, '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', Genomics, vol. 79, no. 3, pp. 413-22. https://doi.org/10.1006/geno.2002.6705

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title = "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",

abstract = "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.",

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author = "Anton Buzdin and Konstantin Khodosevich and Ilgar Mamedov and Tatyana Vinogradova and Yuri Lebedev and Gerhard Hunsmann and Eugene Sverdlov",

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AU - Buzdin, Anton

AU - Khodosevich, Konstantin

AU - Mamedov, Ilgar

AU - Vinogradova, Tatyana

AU - Lebedev, Yuri

AU - Hunsmann, Gerhard

AU - Sverdlov, Eugene

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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.

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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

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DO - 10.1006/geno.2002.6705

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