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Open Access Research article

Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution

David Laperriere12, Tian-Tian Wang3, John H White34* and Sylvie Mader124*

Author Affiliations

1 Department of Biochemistry University of Montreal, Montreal, Québec, H3C 3J7, Canada

2 Institute for Research in Immunology and Cancer, University of Montreal, Montréal, Québec, H3C 3J7, Canada

3 Department of Physiology, McGill University, Montréal, Québec, H3G 1Y6, Canada

4 Department of Medicine, McGill University, Montréal, Québec, H3G 1Y6, Canada

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BMC Genomics 2007, 8:23  doi:10.1186/1471-2164-8-23

Published: 19 January 2007

Abstract

Background

Nuclear receptors are hormone-regulated transcription factors whose signaling controls numerous aspects of development and physiology. Many receptors recognize DNA hormone response elements formed by direct repeats of RGKTCA motifs separated by 1 to 5 bp (DR1-DR5). Although many known such response elements are conserved in the mouse and human genomes, it is unclear to which extent transcriptional regulation by nuclear receptors has evolved specifically in primates.

Results

We have mapped the positions of all consensus DR-type hormone response elements in the human genome, and found that DR2 motifs, recognized by retinoic acid receptors (RARs), are heavily overrepresented (108,582 elements). 90% of these are present in Alu repeats, which also contain lesser numbers of other consensus DRs, including 50% of consensus DR4 motifs. Few DR2s are in potentially mobile AluY elements and the vast majority are also present in chimp and macaque. 95.5% of Alu-DR2s are distributed throughout subclasses of AluS repeats, and arose largely through deamination of a methylated CpG dinucleotide in a non-consensus motif present in AluS sequences. We find that Alu-DR2 motifs are located adjacent to numerous known retinoic acid target genes, and show by chromatin immunoprecipitation assays in squamous carcinoma cells that several of these elements recruit RARs in vivo. These findings are supported by ChIP-on-chip data from retinoic acid-treated HL60 cells revealing RAR binding to several Alu-DR2 motifs.

Conclusion

These data provide strong support for the notion that Alu-mediated expansion of DR elements contributed to the evolution of gene regulation by RARs and other nuclear receptors in primates and humans.