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10.1101/gr.2693004 Access the most recent version at doi: 2004 14: 2245-2252 Genome Res. Alkes L. Price, Eleazar Eskin and Pavel A. Pevzner evolutionary history repeat elements reveals complex Alu Whole-genome analysis of Material Supplemental http://genome.cshlp.org/content/suppl/2004/10/06/14.11.2245.DC1.html References http://genome.cshlp.org/content/14/11/2245.full.html#related-urls Article cited in: http://genome.cshlp.org/content/14/11/2245.full.html#ref-list-1 This article cites 35 articles, 12 of which can be accessed free at: service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box at the http://genome.cshlp.org/subscriptions go to: Genome Research To subscribe to Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press on February 16, 2009 - Published by genome.cshlp.org Downloaded from
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Whole-genome analysis of Alu repeat elements reveals complex evolutionary history Alkes L. Price, 1 Eleazar Eskin, and Pavel A. Pevzner Department of Computer Science and Engineering, University of California–San Diego, La Jolla, California 92093-0114, USA Alu repeats are the most abundant family of repeats in the human genome, with over 1 million copies comprising 10% of the genome. They have been implicated in human genetic disease and in the enrichment of gene-rich segmental duplications in the human genome, and they form a rich fossil record of primate and human history. Alu repeat elements are believed to have arisen from the replication of a small number of source elements, whose evolution over time gives rise to the 31 Alu subfamilies currently reported in Repbase Update. We apply a novel method to identify and statistically validate 213 Alu subfamilies. We build an evolutionary tree of these subfamilies and conclude that the history of Alu evolution is more complex than previous studies had indicated. [Supplemental material is available online at www.genome.org.] Alu repeats are a family of short interspersed elements (SINEs) that replicate via LINE-mediated reverse transcription of an RNA polymerase III transcript (Rogers 1983; Mathias et al. 1991; Dewannieux et al. 2003). Each Alu element is roughly 280 bp long, followed by a poly-A tail of variable length. Thus, the more than 1 million Alu elements comprise roughly 10% of the human genome (International Human Genome Consortium 2001). Al- though Alu repeats have no known biological function (Schmid 2003), the study of the Alu repeat family has many ramifications. Alu insertions and Alu -mediated unequal recombination contrib- ute to a significant proportion of human genetic disease (Dein- inger and Batzer 1999). Alu -mediated unequal recombination is believed to be responsible for the enrichment of gene-rich seg- mental duplications in humans versus other sequenced organ- isms (Bailey et al. 2003). Alu repeats have been used to study the history of substitution patterns in the human genome (Arndt et al. 2003), and polymorphic Alu insertions have been used as markers to determine genetic distances between human sub- populations (Watkins et al. 2003). Recently, a phylogenetic
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