Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes

Abstract

A technique for genome-wide detection of differences in the integration site positions of interspersed repeats in related genomes (DiffIR) is described. The technique is based on a whole- genome selective PCR amplification of the repeats' flanking regions followed by a differential hybridization screening of the arrayed library of the selected amplicons. The technique was successfully applied to the comparison of the integration sites in the human and chimpanzee genomes, allowing us to discover 11 new human-specific integrations of human endogenous retrovirus, K family (HML-2) long terminal repeats.

At Least 50% of Human-Specific HERV-K (HML-2) Long Terminal Repeats Serve In Vivo as Active Promoters for Host Nonrepetitive DNA Transcription

“…Data on insertion polymorphisms of the HS family members in the human and chimpanzee genomes were partly previously reported by us and other authors (2,6,9,11,32,35) and partly obtained using the UCSC genome browser (http://genome.ucsc.edu/cgi-bin/hgGateway, track "chimp").…”

Evolutionary dynamics of endogenous Jaagsiekte sheep retroviruses proliferation in the domestic sheep, mouflon and Pyrenean chamois

“…A fraction of endogenous JSRV flanking 5 0 -LTR sequence was amplified using the selective PCR suppression technique (Siebert et al, 1995;Lebedev et al, 2000;Mamedov et al, 2002). This technique has four main steps: (1) targeted sequences cleaved by a restriction enzyme, (2) ligation of restricted sites with an adapter pair of complementary oligonucleotides of unequal length, (3) amplification of the adapter-containing restricted fragments, and (4) preparation of libraries of amplicons.…”

“…A and T primers (Mamedov et al, 2002; Table 2) were used in the PCR suppression technique. LTR primer (designed and named LTRR by Chessa et al (2009) Inverse PCR.…”

“…Inverse PCR (iPCR) technique has been widely used to identify virus insertion points into the genome or sequences flanking transposable elements; (Ochman et al, 1988) but in 2000, a new technique called PCR suppression was used to detect polymorphic insertions/deletions in the genome of different and unsequenced species, and facilitated the creation of a specific library of these flanking regions (Siebert et al, 1995;Lebedev et al, 2000;Mamedov et al, 2002). In addition, the International Sheep Genomics Consortium recently announced the release of the third build of the sheep reference genome assembly called OARv3.0 (Archibald et al, 2010).…”

A new set of markers for human identification based on 32 polymorphic Alu insertions

“…In the past decade, progress in human genome sequencing and methods of comparative genomics resulted in the identification of a new type of MGMs based on retroelement (RE) insertion polymorphism. [11][12][13][14][15] Recent studies revealed the existence of several thousands of polymorphic RE insertions in the human genome. This type of MGMs has several peculiarities making them attractive for human genetic identification purposes: (i) RE insertions are stable, that is there is no specific mechanism for withdrawing or removing an element from its insertion point; (ii) the probability of independent RE insertion in the same genomic locus is negligibly small, and the presence of RE indicates identity by descent; and (iii) simple identification.…”