MBE Advance Access originally published online on May 30, 2003
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mol. Biol. Evol. 20(8):1349-1361. 2003
DOI: 10.1093/molbev/msg150
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Recently Integrated Alu Elements and Human Genomic Diversity
* Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University
Department of Anatomy, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
Department of Human Genetics, University of Utah Health Sciences Center
E-mail: mbatzer{at}lsu.edu.
A comprehensive analysis of two Alu Y lineage subfamilies was undertaken to assess Alu-associated genomic diversity and identify new Alu insertion polymorphisms for the study of human population genetics. Recently integrated Alu elements (283) from the Yg6 and Yi6 subfamilies were analyzed by polymerase chain reaction (PCR), and 25 of the loci analyzed were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. These newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity. Our screening of the Alu insertion loci also resulted in the recovery of several "young" Alu elements that resided at orthologous positions in nonhuman primate genomes. Sequence analysis demonstrated these "young" Alu insertions were the products of gene conversion events of older, preexisting Alu elements or independent parallel forward insertions of older Alu elements in the same short genomic region. The level of gene conversion between Alu elements suggests that it may have an influence on the single nucleotide polymorphism within Alu elements in the genome. We have also identified two genomic deletions associated with the retroposition and insertion of Alu Y lineage elements into the human genome. This type of Alu retroposition–mediated genomic deletion is a novel source of lineage-specific evolution within primate genomes.
Key Words: primates • deletion • insertion polymorphism • gene conversion
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  V. P. Belancio, D. J. Hedges, and P. Deininger Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health Genome Res., March 1, 2008; 18(3): 343 - 358. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. F. Y. Brookfield and L. J. Johnson The Evolution of Mobile DNAs: When Will Transposons Create Phylogenies That Look As If There Is a Master Gene? Genetics, June 1, 2006; 173(2): 1115 - 1123. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. J. Gentles, O. Kohany, and J. Jurka Evolutionary Diversity and Potential Recombinogenic Role of Integration Targets of Non-LTR Retrotransposons Mol. Biol. Evol., October 1, 2005; 22(10): 1983 - 1991. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Gilbert, S. Lutz, T. A. Morrish, and J. V. Moran Multiple Fates of L1 Retrotransposition Intermediates in Cultured Human Cells Mol. Cell. Biol., September 1, 2005; 25(17): 7780 - 7795. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. N. van de Lagemaat, L. Gagnier, P. Medstrand, and D. L. Mager Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates Genome Res., September 1, 2005; 15(9): 1243 - 1249. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Sandovici, S. Kassovska-Bratinova, J. C. Loredo-Osti, M. Leppert, A. Suarez, R. Stewart, F. D. Bautista, M. Schiraldi, and C. Sapienza Interindividual variability and parent of origin DNA methylation differences at specific human Alu elements Hum. Mol. Genet., August 1, 2005; 14(15): 2135 - 2143. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Han, S. K. Sen, J. Wang, P. A. Callinan, J. Lee, R. Cordaux, P. Liang, and M. A. Batzer Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages Nucleic Acids Res., July 20, 2005; 33(13): 4040 - 4052. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Han, J. Xing, H. Wang, D. J. Hedges, R. K. Garber, R. Cordaux, and M. A. Batzer Under the genomic radar: The Stealth model of Alu amplification Genome Res., May 1, 2005; 15(5): 655 - 664. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. R. Bhangale, M. J. Rieder, R. J. Livingston, and D. A. Nickerson Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes Hum. Mol. Genet., January 1, 2005; 14(1): 59 - 69. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Bennett, L. E. Coleman, C. Tsui, W. S. Pittard, and S. E. Devine Natural Genetic Variation Caused by Transposable Elements in Humans Genetics, October 1, 2004; 168(2): 933 - 951. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Hedges, P. A. Callinan, R. Cordaux, J. Xing, E. Barnes, and M. A. Batzer Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages Genome Res., June 1, 2004; 14(6): 1068 - 1075. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. D. Makova, S. Yang, and F. Chiaromonte Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents Genome Res., April 1, 2004; 14(4): 567 - 573. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Khodosevich, Y. Lebedev, and E. D. Sverdlov Large-scale determination of the methylation status of retrotransposons in different tissues using a methylation tags approach Nucleic Acids Res., February 18, 2004; 32(3): e31 - e31. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A.-H. Salem, D. A. Ray, J. Xing, P. A. Callinan, J. S. Myers, D. J. Hedges, R. K. Garber, D. J. Witherspoon, L. B. Jorde, and M. A. Batzer Alu elements and hominid phylogenetics PNAS, October 28, 2003; 100(22): 12787 - 12791. [Abstract] [Full Text] [PDF]
|
|