Genome-wide target site triplication of Alu elements in the human genome Wooseok Lee1, Seyoung Mun1,2, Keunsoo Kang3, Lothar Hennighausen2, and Kyudong Han1,4,* 1 Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea. 2 Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. 3 4 Department of Microbiology, Dankook University, Cheonan 330-714, Korea. DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 330-714, Republic of Korea. Alu elements are the most successful short interspersed elements in primate genomes and their retrotransposition is a major sources of genomic expansion. Alu elements integrate into genomic regions through target-site primed reverse transcription, which generates target site duplications (TSDs). Unexpectedly, we have identified target site triplications (TST) at some loci, where two Alu elements in tandem share one direct repeat. Thus, the three copies of the repeat are present. We located 214 TST loci in the human genome and examined 27 putative human-specific TST loci using PCR validation. As a result, 14 human-specific TST loci were identified. These findings suggest that unequal homologous recombination between TSDs can lead to TST. Through this mechanism, the copy number of Alu elements could have increased in primate genomes without new Alu retrotransposition events. This study provides new insight into the augmentation of Alu elements in the primate genome.