Supplementary Material for: Alu-Alu Fusion Sequences Identified at Junction Sites of Copy Number Amplified Regions in Cancer Cell Lines

2012-09-14T00:00:00Z (GMT) by Kitada K. Aikawa S. Aida S.
<i>Alu</i> elements are short, ∼300-bp stretches of DNA and are the most abundant repetitive elements in the human genome. A large number of chromosomal rearrangements mediated by <i>Alu-Alu </i>recombination have been reported in germline cells, but only a few in somatic cells. Cancer development is frequently accompanied by various chromosomal rearrangements including gene amplification. To explore an involvement of <i>Alu-Alu</i> fusion in gene amplification events, we determined 20 junction site sequences of 5 highly amplified regions in 4 cancer cell lines. The amplified regions exhibited a common copy number profile: a stair-like increase with multiple segments, which is implicated in the breakage-fusion-bridge (BFB) cycle-mediated amplification. All of the sequences determined were characterized as head-to-head or tail-to-tail fusion of sequences separated by 1–5 kb in the genome sequence. Of these, 4 junction site sequences were identified as <i>Alu-Alu</i> fusions between inverted, paired <i>Alu</i> elements with relatively long overlapping sequences of 17, 21, 22, and 24 bp. Together with genome mapping data of <i>Alu</i> elements, these findings suggest that when breakages occur at or near inverted, paired <i>Alu</i> elements in the process of BFB cycle-mediated amplification, sequence homology of <i>Alu</i> elements is frequently used to repair the broken ends.