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PMID: 15867427 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Under the genomic radar: the stealth model of Alu amplification.

Genome research ·Vol. 15 ·No. 5 ·2005-05-00 ·Pages 655-64

Han K, Xing J, Wang H, Hedges DJ, Garber RK, Cordaux R, Batzer MA

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.

MeSH Terms
Alu Elements/genetics Animals Base Sequence Computational Biology DNA Primers Electrophoresis, Agar Gel Evolution, Molecular Genome, Human Humans Models, Genetic Molecular Sequence Data Oligonucleotides Phylogeny Primates/genetics Sequence Analysis, DNA Species Specificity
Chemicals
DNA Primers Oligonucleotides
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Han Kyudong
Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
Xing Jinchuan
Wang Hui
Hedges Dale J
Garber Randall K
Cordaux Richard
Batzer Mark A
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.3492605
Published
2005-05-00
Pages
655-64
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC1088293
Subset
IM
Grants
NIGMS NIH HHS · R01 GM059290 · United States
NIGMS NIH HHS · R01 GM 59290 · United States
Databases
GENBANK
AY791249, AY791250, AY791251, AY791252, AY791253, AY791254, AY791255, AY791256, AY791257, AY791258, AY791259, AY791260, AY791261, AY791262, AY791263, AY791264, AY791265, AY791266, AY791267, AY791268, AY791269, AY791270, AY791271, AY791272, AY791273, AY791274, AY791275, AY791276, AY791277, AY791278, AY791279, AY791280, AY791281, AY791282, AY791283, AY791284, AY791285, AY791286, AY791287, AY791288, AY791289, AY791290
External Links
PubMed source DOI: 10.1101/gr.3492605 PMC Full Text View journal details
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