| Summary: | <p>Abstract</p> <p>Background</p> <p>Recombination rates vary widely across the human genome, but little of that variation is correlated with known DNA sequence features. The genome contains more than one million <it>Alu </it>mobile element insertions, and these insertions have been implicated in non-homologous recombination, modulation of DNA methylation, and transcriptional regulation. If individual <it>Alu </it>insertions have even modest effects on local recombination rates, they could collectively have a significant impact on the pattern of linkage disequilibrium in the human genome and on the evolution of the <it>Alu </it>family itself.</p> <p>Results</p> <p>We carried out sequencing, SNP identification, and SNP genotyping around 19 <it>AluY </it>insertion loci in 347 individuals sampled from diverse populations, then used the SNP genotypes to estimate local recombination rates around the <it>AluY </it>loci. The loci and SNPs were chosen so as to minimize other factors (such as SNP ascertainment bias and SNP density) that could influence recombination rate estimates. We detected a significant increase in recombination rate within ~2 kb of the <it>AluY </it>insertions in our African population sample. To test this observation against a larger set of <it>AluY </it>insertions, we applied our locus- and SNP-selection design and analyses to the HapMap Phase II data. In that data set, we observed a significantly increased recombination rate near <it>AluY </it>insertions in both the CEU and YRI populations.</p> <p>Conclusion</p> <p>We show that the presence of a fixed <it>AluY </it>insertion is significantly predictive of an elevated local recombination rate within 2 kb of the insertion, independent of other known predictors. The magnitude of this effect, approximately a 6% increase, is comparable to the effects of some recombinogenic DNA sequence motifs identified via their association with recombination hot spots.</p>
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