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Nucleic Acids Research, 2002, Vol. 30, No. 14 e71
© 2002 Oxford University Press

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

Ilgar Mamedov*, Anastasia Batrak, Anton Buzdin, Elena Arzumanyan, Yuri Lebedev and Eugene D. Sverdlov

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, 117997 Moscow, Russia

*To whom correspondence should be addressed. Tel: +7 95 330 69 92; Fax: +7 95 330 65 38; Email: imam{at}humgen.siobc.ras.ru

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.


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