Alu pair exclusions in the human genome

We performed a comprehensive analysis of all (> 800,000) full-length Alu elements in the human genome. This large sample size permits detection of small differences in the ratio between inverted and direct Alu pairs (I:D). We have discovered a significant depression in the full-length Alu pair I:D ratio that extends to repeat pairs separated by ≤ 350,000 bp. Within this imbalance bubble (those Alu pairs separated by ≤ 350,000 bp), direct pairs outnumber inverted pairs. Using PCR, we experimentally verified several examples of inverted Alu pair exclusions that were caused by deletions.Over 50 million full-length Alu pairs reside within the I:D imbalance bubble. Their collective impact may represent one source of Alu element-related human genomic instability that has not been previously characterized.Retrotransposons are mobile DNA elements that populate genomes via their respective RNA transcripts. The retrotransposon with the highest copy number in the human genome is the Alu element [1]. Alu elements lack the necessary repertoire of enzymes to effect their independent insertion and are thus classified as non-autonomous mobile elements. For recent reviews, see [2-4].Following transcription, Alu RNA is thought to require the assistance of the LINE1 open reading frame 2 protein (ORF2p) both for nicking the genome at the insertion site and for reverse transcription of the Alu RNA transcript [5,6]. The endonuclease and reverse transcriptase functions of ORF2p are referred to as L1EN and L1RT, respectively. While L1EN has been shown to have some tolerance for target site variation, it most frequently cleaves at the T/A transition within the sequence, 5'-TTTTAA-3' [7-10]. Following cleavage, the poly-T sequence of the target site becomes accessible to the complementary poly(A) tail of Alu RNA. Hybridization of these two sequences results in a short RNA-DNA hybrid that both orients the RNA transcript and primes reverse transcription of the Alu RNA by L1RT. Identical sequen