Beyond the Identification of Transcribed Sequences:
Functional, Evolutionary and Expression Analysis
12th International Workshop
October 25-28, 2002
Washington, DC

List of Abstracts * Speakers * Organizers * Authors * Original Announcement

Genome-Wide Identification of Differences in the Retroelement Integrations between Humans and Chimpanzees

E. Sverdlov, A. Buzdin, I. Mamedov, S. Ustugova, E. Gogvadze, Yu.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 RUSSIA
Telephone: 7 (095) 330 6529
Fax: 7 (095) 330 6538

Lebedev Sequences derived from transposable elements transposing through RNA intermediates (retroelements, REs) - long interspersed elements (LINEs), short interspersed elements (SINEs), LTR retrotransposons - comprise 13, 20, and 8% of the genome, respectively. They may play an important role in speciation of Hominoids providing new regulatory modules capable of changing gene expression networks. The identification of human specific integrations in the vicinity of human genes could reveal candidate regulatory elements within REs capable of affecting gene regulation and thus influencing the split of the human and other hominoid lineages. We have developed a method of Targeted Genomic Difference Analysis (TGDA) for genome-wide detection of differences in integration sites of interspersed repeats between related genomes. The method includes two principal steps: (i) a whole genome selective amplification of the flanks adjacent to target interspersed repetitive elements in both genomic DNAs under comparison, and (ii) subtractive hybridization of the selected amplicons. Differences between the human and chimpanzee genomes in the integration sites of HERV-K (HML-2) retroviruses and related solitary long terminal repeats (LTRs) were analyzed. Of 55 sequenced clones randomly chosen from a library enriched with human specific integration (HSI) sites, 33 (60%) represented HSIs. Together with HSIs described by other authors, the number of characterized LTR HSIs is increased to 40. Using these 40 human-specific LTR sequences, we have derived a consensus sequence for an evolutionary young HERV-K LTRs named the HS family. In the human genome the HS family is represented by ~150 LTR sequences, 90% of them being human-specific. The family can be subdivided into two subfamilies of 5.8 and 10.3 Myr evolutionary ages. We found human-specific HERV-K LTRs integrations in introns of 17 human genes, most of which being oriented in the opposite orientation with regard to the direction of gene transcription. TGDA has been applied also to genome-wide screening of human specific L1 integrations and their polymorphisms. We obtained a library highly enriched in human specific L1 insertions, and identified 24 new such insertions. Many of these insertions are polymorphic in human populations. The results suggest that TGDA is a universal method that can be successfully used for the detection of evolutionary and polymorphic markers in any closely related genomes. The research was supported by INTAS-01-0759, RFBR 00-15-97945 and RFBR 02-04-48614 grants, and by contract of the Ministry of Industry, Science and Technology of the Russian Federation.

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