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MBE Advance Access published online on March 25, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn071
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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

Retrotransposition as a Source of New Promoters

Kohji Okamura* and Kenta Nakai*,{dagger}

* Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
{dagger} Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan

Corresponding author: Kenta Nakai, Human Genome Centre, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato Ward, Tokyo 108-8639, Japan, +81-3-5449-5131 (phone), +81-3-5449-5133 (facsimile), knakai{at}ims.u-tokyo.ac.jp

Received for publication December 20, 2007. Revision received March 14, 2008. Accepted for publication March 18, 2008.

The fact that promoters are essential for the function of all genes presents the basis of the general idea that retrotranspositions give rise to processed pseudogenes. However, recent studies have demonstrated that some retrotransposed genes are transcriptionally active. Because promoters are not thought to be retrotransposed along with exonic sequences, these transcriptionally active genes must have acquired a functional promoter by mechanisms that are yet to be determined. Hence, comparison between a retrotransposed gene and its source gene appears to provide a unique opportunity to investigate the promoter creation for a new gene. Here, we identified 29 gene pairs in the human genome, consisting of a functional retrotransposed gene and its parental gene, and compared their respective promoters. In more than half of these cases, we unexpectedly found that a large part of the core promoter had been transcribed, reverse-transcribed, and then integrated to be operative at the transposed locus. This observation can be ascribed to the recent discovery that transcription start sites tend to be interspersed rather than situated at one specific site. This propensity could confer retrotransposability to promoters per se. Accordingly, the retrotransposability can explain the genesis of some alternative promoters.

Key Words: promoter • transcription start site • retrotransposition • alternative promoter • human genome • molecular evolution


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