Genome-wide targeted search for human specific and polymorphic L1 integrations
- 25 February 2003
- journal article
- research article
- Published by Springer Science and Business Media LLC in Human Genetics
- Vol. 112 (5-6), 527-533
- https://doi.org/10.1007/s00439-002-0904-2
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 ~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.Keywords
This publication has 29 references indexed in Scilit:
- A Comprehensive Analysis of Recently Integrated Human Ta L1 ElementsAmerican Journal of Human Genetics, 2002
- Twin Priming: A Proposed Mechanism for the Creation of Inversions in L1 RetrotranspositionGenome Research, 2001
- Genomic Characterization of Recent Human LINE-1 Insertions: Evidence Supporting Random InsertionGenome Research, 2001
- Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversityJournal of Molecular Biology, 2001
- The Sequence of the Human GenomeScience, 2001
- Initial sequencing and analysis of the human genomeNature, 2001
- Structural evidence of genomic exon-deletion mediated byAlu-Alu recombination in a human case with heme oxygenase-1 deficiencyHuman Mutation, 2000
- Transduction of 3'-flanking sequences is common in L1 retrotranspositionHuman Molecular Genetics, 2000
- The impact of L1 retrotransposons on the human genomeNature Genetics, 1998
- Ancestral, Mammalian-wide Subfamilies of LINE-1 Repetitive SequencesJournal of Molecular Biology, 1995