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MBE Advance Access originally published online on November 4, 2008
Molecular Biology and Evolution 2009 26(2):327-334; 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 Articles

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

Chongjian Chen*,{dagger}, Takeshi Ara{ddagger} and Daniel Gautheret*

* Institut de Génétique et Microbiologie, Université Paris-Sud 11, CNRS UMR 8621, Orsay, France
{dagger} Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Zhongshan University, Guangzhou, People's republic of China
{ddagger} Kazusa DNA Research Institute, Kisarazu, Chiba, Japan

E-mail: daniel.gautheret{at}u-psud.fr.

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 (PASs). Strikingly, although Alu’s 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 Alu’s reflects a radical difference in the fitness of sense and antisense Alu’s toward cleavage/polyadenylation activity. In contrast to previous beliefs, Alu inserts do not necessarily represent weak or cryptic PASs; instead, they often constitute the major or the unique PAS in a gene, adding to the growing list of Alu exaptations. Finally, some Alu-borne PASs are intronic and produce truncated transcripts that may impact gene function and/or contribute to gene remodeling.

Key Words: polyadenylation • retroposons • Alu • SINE

Dan Graur, Associate Editor


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