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Vol. 10, Issue 10, 1485-1495, October 2000

Potential Gene Conversion and Source Genes for Recently Integrated Alu Elements

Astrid M. Roy,1,6 Marion L. Carroll,2,6 Son V. Nguyen,2 Abdel-Halim Salem,2 Michael Oldridge,3 Andrew O. M. Wilkie,3,4 Mark A. Batzer,2,7 and Prescott L. Deininger1,5,7,8

1 Tulane Cancer Center, Department of Environmental Health Sciences, Tulane University Medical Center, New Orleans, Louisiana 70112, USA; 2 Departments of Pathology, Biometry and Genetics, Biochemistry, and Molecular Biology, Stanley S. Scott Cancer Center, Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA; 3 Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX2 6HE, UK; 4 Oxford Craniofacial Unit, The Radcliffe Infirmary NHS Trust, Oxford OX2 6HE, UK; 5 Laboratory of Molecular Genetics, Alton Ochsner Medical Foundation, New Orleans, Louisiana 70121, USA

Alu elements comprise >10% of the human genome. We have used a computational biology approach to analyze the human genomic DNA sequence databases to determine the impact of gene conversion on the sequence diversity of recently integrated Alu elements and to identify Alu elements that were potentially retroposition competent. We analyzed 269 Alu Ya5 elements and identified 23 members of a new Alu subfamily termed Ya5a2 with an estimated copy number of 35 members, including the de novo Alu insertion in the NF1 gene. Our analysis of Alu elements containing one to four (Ya1-Ya4) of the Ya5 subfamily-specific mutations suggests that gene conversion contributed as much as 10%-20% of the variation between recently integrated Alu elements. In addition, analysis of the middle A-rich region of the different Alu Ya5 members indicates a tendency toward expansion of this region and subsequent generation of simple sequence repeats. Mining the databases for putative retroposition-competent elements that share 100% nucleotide identity to the previously reported de novo Alu insertions linked to human diseases resulted in the retrieval of 13 exact matches to the NF1 Alu repeat, three to the Alu element in BRCA2, and one to the Alu element in FGFR2 (Apert syndrome). Transient transfections of the potential source gene for the Apert's Alu with its endogenous flanking genomic sequences demonstrated the transcriptional and presumptive transpositional competency of the element.

6 These authors contributed equally to this work.

7 These authors contributed equally to this work as senior authors.

8 Corresponding author.

10:1485-1495 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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