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MBE Advance Access first published online on November 4, 2008
This version published online on November 7, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn249
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Using Alu Elements as Polyadenylation Sites: A Case of Retroposon Exaptation

Chongjian Chen1,2, Takeshi Ara3 and Daniel Gautheret1,4

1 Université Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, 91400 Orsay, France
2 Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Zhongshan University, Guangzhou 510275, People's Republic of China
3 Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan

4 To whom correspondence should be addressed. Tel: + 33 1 69 15 46 32; Fax: +33 1 69 15 46 29; Email: daniel.gautheret{at}u-psud.fr

Received for publication September 11, 2008. Revision received October 23, 2008. Accepted for publication October 27, 2008.

Of the 1.1 million Alu retroposons in the human genome, about 10,000 are inserted in the 3’ untranslated regions (UTR) of protein-coding genes and 1% of these (107 events) are active as polyadenylation sites. Strikingly, while Alus in 3’ UTR are indifferently inserted in the forward or reverse direction, 99% of polyadenylation-active Alu sequences are forward-oriented. Consensus Alu+ sequences contain sites that can give rise to polyadenylation signals and enhancers through a few point mutations. We found that the strand bias of polyadenylation-active Alus reflects a radical difference in the fitness of sense and antisense Alus towards cleavage/polyadenylation activity. In contrast to previous beliefs, Alu inserts do not necessarily represent weak or cryptic polyadenylation sites; instead they often constitute the major or the unique polyadenylation site in a gene, adding to the growing list of Alu exaptations. Finally, some Alu-borne polyadenylation sites are intronic and produce truncated transcripts that may impact gene function and/or contribute to gene remodeling.

Key Words: polyadenylation • retroposons • Alu • SINE


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