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The Distribution of L1 and Alu Retroelements in Relation to GC Content on Human Sex Chromosomes Is Consistent with the Ectopic Recombination Model

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Abstract

The distribution of Alu and L1 retroelements in the human genome changes with their age. Active retroelements target AT-rich regions, but their frequency increases in GC- and gene-rich regions of the genome with increasing age of the insertions. Currently there is no consensus on the mechanism generating this pattern. In this paper we test the hypothesis that selection against deleterious deletions caused by ectopic recombination between repeats is the main cause of the inhomogeneous distribution of L1s and Alus, by means of a detailed analysis of the GC distribution of the repeats on the sex chromosomes. We show that (1) unlike on the autosomes and X chromosome, L1s do not accumulate on the Y chromosome in GC-rich regions, whereas Alus accumulate there to a minor extent; (2) on the Y chromosome Alu and L1 densities are positively correlated, unlike the negative correlation on other chromosomes; and (3) in gene-poor regions of chromosome 4 and X, the distribution of Alus and L1s does not shift toward GC-rich regions. In addition, we show that although local GC content of long L1 insertions is lower than average, their selective loss from recombining chromosomes is not the main cause of the enrichment of ancient L1s in GC-rich regions. The results support the hypothesis that ectopic recombination causes the shift of Alu and L1 distributions toward the gene-rich regions of the genome.

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Acknowledgments

We thank Deborah Charlesworth and both anonymous referees for their constructive reviews, which greatly improved the manuscript, and Thorsten Reusch and Edward Brede for their critical reading of an early draft of this paper. G.A. was supported by a postdoctoral fellowship from the Alexander von Humboldt Foundation and the Max Planck Society.

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  1. Max Planck Institute of Limnology, Department of Ecophysiology, August Thienemann Str. 2, 24306, Plön, Germany

    György Abrusán & Hans-Jürgen Krambeck

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  1. György Abrusán
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  2. Hans-Jürgen Krambeck
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Correspondence to György Abrusán.

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Reviewing Editor: Dr. Deborah Charlesworth

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Abrusán, G., Krambeck, HJ. The Distribution of L1 and Alu Retroelements in Relation to GC Content on Human Sex Chromosomes Is Consistent with the Ectopic Recombination Model. J Mol Evol 63, 484–492 (2006). https://doi.org/10.1007/s00239-005-0275-0

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  • DOI: https://doi.org/10.1007/s00239-005-0275-0

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