title: Under the genomic radar: the stealth model of Alu amplification.
abstract: Alu elements are the most successful SINEs (Short INterspersed Elements) in primate genomes and have reached more than 1,000,000 copies in the human genome. The amplification of most Alu elements is thought to occur through a limited number of hyperactive "master" genes that produce a high number of copies during long evolutionary periods of time. However, the existence of long-lived, low-activity Alu lineages in the human genome suggests a more complex propagation mechanism. Using both computational and wet-bench approaches, we reconstructed the evolutionary history of the AluYb lineage, one of the most active Alu lineages in the human genome. We show that the major AluYb lineage expansion in humans is a species-specific event, as nonhuman primates possess only a handful of AluYb elements. However, the oldest existing AluYb element resided in an orthologous position in all hominoid primate genomes examined, demonstrating that the AluYb lineage originated 18-25 million years ago. Thus, the history of the AluYb lineage is characterized by approximately 20 million years of retrotranspositional quiescence preceding a major expansion in the human genome within the past few million years. We suggest that the evolutionary success of the Alu family may be driven at least in part by "stealth-driver" elements that maintain low retrotranspositional activity over extended periods of time and occasionally produce short-lived hyperactive copies responsible for the formation and remarkable expansion of Alu elements within the genome.
authors.affiliation: Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Kyudong
authors.initials: K
authors.lastname: Han
authors.forename: Jinchuan
authors.initials: J
authors.lastname: Xing
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.forename: Dale J
authors.initials: DJ
authors.lastname: Hedges
authors.forename: Randall K
authors.initials: RK
authors.lastname: Garber
authors.forename: Richard
authors.initials: R
authors.lastname: Cordaux
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D017931:DNA Primers; D004587:Electrophoresis, Agar Gel; D019143:Evolution, Molecular; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009841:Oligonucleotides; D010802:Phylogeny; D011323:Primates / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D009841:Oligonucleotides