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.
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. anton@humgen.siobc.ras.ru
authors.forename: Anton
authors.initials: A
authors.lastname: Buzdin
authors.forename: Konstantin
authors.initials: K
authors.lastname: Khodosevich
authors.forename: Ilgar
authors.initials: I
authors.lastname: Mamedov
authors.forename: Tatyana
authors.initials: T
authors.lastname: Vinogradova
authors.forename: Yuri
authors.initials: Y
authors.lastname: Lebedev
authors.forename: Gerhard
authors.initials: G
authors.lastname: Hunsmann
authors.forename: Eugene
authors.initials: E
authors.lastname: Sverdlov
mesh_terms: D000818:Animals; D001483:Base Sequence; D020077:Endogenous Retroviruses / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000235:genetics; D010802:Phylogeny; D013045:Species Specificity; D020079:Terminal Repeat Sequences / Q000235:genetics