Alu repeats increase local recombination rates

David J Witherspoon,Yuhua Zhang,W Scott Watkins,Dale J Hedges,Whitney L Tolpinrud,Lynn B Jorde,Mark A Batzer,Jinchuan Xing

doi:10.1186/1471-2164-10-530

David J Witherspoon, Yuhua Zhang + Show 6 more

Open Access

https://doi.org/10.1186/1471-2164-10-530

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Abstract

BackgroundRecombination 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 Alu mobile element insertions, and these insertions have been implicated in non-homologous recombination, modulation of DNA methylation, and transcriptional regulation. If individual Alu 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 Alu family itself.ResultsWe carried out sequencing, SNP identification, and SNP genotyping around 19 AluY insertion loci in 347 individuals sampled from diverse populations, then used the SNP genotypes to estimate local recombination rates around the AluY 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 AluY insertions in our African population sample. To test this observation against a larger set of AluY 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 AluY insertions in both the CEU and YRI populations.ConclusionWe show that the presence of a fixed AluY 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.

Highlights

Recombination rates vary widely across the human genome, but little of that variation is correlated with known DNA sequence features
It has been suggested that polymorphic Alu insertions may suppress recombination when found in the heterozygous state [12], and fixed Alu insertions may contain specific DNA sequence features capable of recruiting recombination-enhancing or -suppressing factors
Our question is: does the presence of an AluY insertion affect the local rate of recombination? We show that the presence of a fixed, young AluY insertion is significantly predictive of a modestly elevated local recombination rate

Summary

Introduction

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 Alu mobile element insertions, and these insertions have been implicated in nonhomologous recombination, modulation of DNA methylation, and transcriptional regulation. BMC Genomics 2009, 10:530 http://www.biomedcentral.com/1471-2164/10/530 tical to each other Their recombinogenic impact is evident: these scattered homologies trigger non-allelic homologous recombination (NAHR) events that lead to translocations, deletions, duplications, and other chromosomal abnormalities and copy number variations [26]. These events have affected the long-term evolution of the human genome and of the Alu insertions themselves [7,8,9,10,11]. It has been suggested that polymorphic Alu insertions may suppress recombination when found in the heterozygous state [12], and fixed Alu insertions may contain specific DNA sequence features capable of recruiting recombination-enhancing or -suppressing factors

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