Recently integrated human Alu repeats: finding needles in the haystack

Citation
Am. Roy et al., Recently integrated human Alu repeats: finding needles in the haystack, GENETICA, 107(1-3), 1999, pp. 149-161
Citations number
33
Categorie Soggetti
Molecular Biology & Genetics
Journal title
GENETICA
ISSN journal
00166707 → ACNP
Volume
107
Issue
1-3
Year of publication
1999
Pages
149 - 161
Database
ISI
SICI code
0016-6707(1999)107:1-3<149:RIHARF>2.0.ZU;2-R
Abstract
Alu elements undergo amplification through retroposition and integration in to new locations throughout primate genomes. Over 500,000 Alu elements resi de in the human genome, making the identification of newly inserted Alu rep eats the genomic equivalent of finding needles in the haystack. Here, we pr esent two complementary methods for rapid detection of newly integrated Alu elements. In the first approach we employ computational biology to mine th e human genomic DNA sequence databases in order to identify recently integr ated Alu elements. The second method is based on an anchor-PCR technique wh ich we term Allele-Specific Alu PCR (ASAP). In this approach, Alu elements are selectively amplified from anchored DNA generating a display or 'finger print' of recently integrated Alu elements. Alu insertion polymorphisms are then detected by comparison of the DNA fingerprints generated from differe nt samples. Here, we explore the utility of these methods by applying them to the identification of members of the smallest previously identified subf amily of Alu repeats in the human genome termed Ya8. This subfamily of Alu repeats is composed of about 50 elements within the human genome. Approxima tely 50% of the Ya8 Alu family members have inserted in the human genome so recently that they are polymorphic, making them useful markers for the stu dy of human evolution.