Genome-wide targeted search for human specific and polymorphic L1 integrations.

Abstract:

:Retroelements (REs) occupy up to 40% of the human genome. Newly integrated REs can change the pattern of expression of pre-existing host genes and therefore might play a significant role in evolution. In particular, human- and primate-specific REs could affect the divergence of the Hominoidea superfamily. A comparative genome-wide analysis of RE sites of integration, neighboring genes, and their regulatory interplay in human and ape genomes would be of help in understanding the impact of REs on evolution and genome regulation. We have developed a technique for the genome-wide comparison of the integrations of transposable elements in genomic DNAs of closely related species. The technique called targeted genome differences analysis (TGDA) is also useful for the detection of deletion/insertion polymorphisms of REs. The technique is based on an enhanced version of subtractive hybridization and does not require preliminary knowledge of the genome sequences under comparison. In this report, we describe its application to the detection and analysis of human specific L1 integrations and their polymorphisms. We obtained a library highly enriched in human-specific L1 insertions and identified 24 such new insertions. Many of these insertions are polymorphic in human populations. The total number of human-specific L1 inserts was estimated to be approximately 4000. 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.

journal_name

Hum Genet

journal_title

Human genetics

authors

Buzdin A,Ustyugova S,Gogvadze E,Lebedev Y,Hunsmann G,Sverdlov E

doi

10.1007/s00439-002-0904-2

keywords:

subject

Has Abstract

pub_date

2003-05-01 00:00:00

pages

527-33

issue

5-6

eissn

0340-6717

issn

1432-1203

journal_volume

112

pub_type

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