title: Analysis of the human Alu Ye lineage.
abstract: BACKGROUND
  Alu elements are short (approximately 300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and function of primate genomes. Approximately 10 % of the mass of the human genome is comprised of Alu elements, making them the most abundant short interspersed element (SINE) in our genome. The majority of Alu amplification occurred early in primate evolution, and the current rate of Alu retroposition is at least 100 fold slower than the peak of amplification that occurred 30-50 million years ago. Alu elements are therefore a rich source of inter- and intra-species primate genomic variation.
  
  
  RESULTS
  A total of 153 Alu elements from the Ye subfamily were extracted from the draft sequence of the human genome. Analysis of these elements resulted in the discovery of two new Alu subfamilies, Ye4 and Ye6, complementing the previously described Ye5 subfamily. DNA sequence analysis of each of the Alu Ye subfamilies yielded average age estimates of approximately 14, approximately 13 and approximately 9.5 million years old for the Alu Ye4, Ye5 and Ye6 subfamilies, respectively. In addition, 120 Alu Ye4, Ye5 and Ye6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and levels of human genomic diversity.
  
  
  CONCLUSIONS
  The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Detailed sequence analysis of several Alu pre-integration sites indicated that multiple types of events had occurred, including gene conversions, near-parallel independent insertions of different Alu elements and Alu-mediated genomic deletions. A potential hotspot for Alu insertion in the Fer1L3 gene on chromosome 10 was also identified.
authors.affiliation: Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA. adeifalla@lsu.edu <adeifalla@lsu.edu>
authors.forename: Abdel-Halim
authors.initials: AH
authors.lastname: Salem
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
authors.forename: Dale J
authors.initials: DJ
authors.lastname: Hedges
authors.forename: Jerzy
authors.initials: J
authors.lastname: Jurka
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D020087:Alu Elements; D000818:Animals; D005075:Biological Evolution; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D017353:Gene Deletion; D014644:Genetic Variation; D016678:Genome; D015894:Genome, Human; D015186:Hominidae; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012984:Software
references.citation: J Mol Biol. 1995 Mar 31;247(3):418-27
references.pmid: 7714898
references.citation: Nucleic Acids Res. 1991 Jul 11;19(13):3619-23
references.pmid: 1649453
references.citation: Cell. 1996 Nov 29;87(5):905-16
references.pmid: 8945517
references.citation: Nat Genet. 2003 Sep;35(1):41-8
references.pmid: 12897783
references.citation: Nucleic Acids Res. 1980 Apr 11;8(7):1499-504
references.pmid: 6253938
references.citation: Cell. 2002 Aug 9;110(3):315-25
references.pmid: 12176319
references.citation: J Mol Evol. 1987;26(3):180-6
references.pmid: 3129565
references.citation: Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11399-404
references.pmid: 11562455
references.citation: Genetics. 2001 Feb;157(2):777-84
references.pmid: 11156996
references.citation: Ann Hum Biol. 2002 May-Jun;29(3):334-47
references.pmid: 12031142
references.citation: Hum Genomics. 2004 Mar;1(3):167-78
references.pmid: 15588477
references.citation: J Mol Biol. 2004 Nov 26;344(3):675-82
references.pmid: 15533437
references.citation: Cell. 2002 Nov 1;111(3):433-44
references.pmid: 12419252
references.citation: Genetics. 2001 Sep;159(1):279-90
references.pmid: 11560904
references.citation: Genomics. 1991 Mar;9(3):481-7
references.pmid: 1851725
references.citation: Am J Hum Genet. 2002 Aug;71(2):312-26
references.pmid: 12070800
references.citation: Trends Genet. 1992 Sep;8(9):307-11
references.pmid: 1365396
references.citation: Nucleic Acids Res. 1990 Dec 11;18(23):6793-8
references.pmid: 2175877
references.citation: Mol Phylogenet Evol. 2003 Mar;26(3):490-501
references.pmid: 12644406
references.citation: Mol Biol Evol. 2003 Aug;20(8):1338-48
references.pmid: 12777507
references.citation: Mol Biol Evol. 1987 Jan;4(1):19-29
references.pmid: 3128713
references.citation: J Mol Evol. 1993 Dec;37(6):566-72
references.pmid: 8114109
references.citation: J Mol Evol. 1996 Jan;42(1):59-65
references.pmid: 8576965
references.citation: Biochim Biophys Acta. 1995 Jul 25;1263(1):99-102
references.pmid: 7632743
references.citation: Cytogenet Genome Res. 2005;108(1-3):63-72
references.pmid: 15545717
references.citation: Mol Phylogenet Evol. 1998 Jun;9(3):585-98
references.pmid: 9668008
references.citation: Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3607-11
references.pmid: 8170955
references.citation: Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1872-7
references.pmid: 9050872
references.citation: Theor Popul Biol. 2002 Jun;61(4):519-30
references.pmid: 12167372
references.citation: J Mol Biol. 1992 Aug 5;226(3):689-706
references.pmid: 1507221
references.citation: Mol Genet Metab. 1999 Jul;67(3):183-93
references.pmid: 10381326
references.citation: Genome Res. 1996 Nov;6(11):1084-92
references.pmid: 8938432
references.citation: J Mol Biol. 1998 Sep 4;281(5):843-56
references.pmid: 9719639
references.citation: Proc Natl Acad Sci U S A. 2004 Jul 20;101(29):10650-4
references.pmid: 15249661
references.citation: Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7
references.pmid: 271968
references.citation: J Mol Biol. 2004 Sep 3;342(1):109-18
references.pmid: 15313610
references.citation: Nat Genet. 1998 May;19(1):19-24
references.pmid: 9590283
references.citation: Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12787-91
references.pmid: 14561894
references.citation: J Mol Evol. 1991 Oct;33(4):311-20
references.pmid: 1774786
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Annu Rev Biochem. 1986;55:631-61
references.pmid: 2427017
references.citation: Nucleic Acids Res. 1989 Apr 11;17(7):2477-91
references.pmid: 2541408
references.citation: Bioessays. 2000 Feb;22(2):148-60
references.pmid: 10655034
references.citation: Cell. 2002 Aug 9;110(3):277-80
references.pmid: 12176313
references.citation: J Mol Biol. 2001 May 11;308(4):587-96
references.pmid: 11350162
references.citation: Genetica. 1999;107(1-3):149-61
references.pmid: 10952208
references.citation: Proc Natl Acad Sci U S A. 1988 Jul;85(13):4770-4
references.pmid: 3387437
references.citation: Mol Biol Evol. 2003 Aug;20(8):1349-61
references.pmid: 12777511
references.citation: J Mol Biol. 2000 Jun 16;299(4):931-9
references.pmid: 10843848
references.citation: J Mol Biol. 2002 Mar 8;316(5):1033-40
references.pmid: 11884141
references.citation: Mutat Res. 2002 Apr 25;501(1-2):137-41
references.pmid: 11934445
references.citation: Trends Ecol Evol. 2004 Oct;19(10):545-53
references.pmid: 16701320
references.citation: Mamm Genome. 1998 May;9(5):355-60
references.pmid: 9545491
references.citation: Science. 1987 Oct 16;238(4825):369-73
references.pmid: 3116671
references.citation: Cytogenet Genome Res. 2005;108(1-3):26-37
references.pmid: 15545713
references.citation: J Mol Biol. 2001 Aug 3;311(1):17-40
references.pmid: 11469855
references.citation: Genome Res. 2000 Oct;10(10):1485-95
references.pmid: 11042148
references.citation: Proc Natl Acad Sci U S A. 1988 Jul;85(13):4775-8
references.pmid: 3387438
references.citation: Cell. 1993 Feb 26;72(4):595-605
references.pmid: 7679954
references.citation: Mol Biol Evol. 1988 Jan;5(1):1-20
references.pmid: 3357413
references.citation: Mol Phylogenet Evol. 2005 Apr;35(1):117-26
references.pmid: 15737586
references.citation: Nat Genet. 1997 May;16(1):6-7
references.pmid: 9140383
references.citation: Nat Rev Genet. 2002 May;3(5):370-9
references.pmid: 11988762
references.citation: J Mol Biol. 1999 Jun 18;289(4):861-71
references.pmid: 10369767
references.citation: J Mol Evol. 1996 Jan;42(1):3-6
references.pmid: 8576960
references.citation: Mol Cell Biol. 1995 Jan;15(1):19-25
references.pmid: 7799926
references.citation: Gene. 1995 Oct 3;163(2):273-8
references.pmid: 7590280
references.citation: J Mol Biol. 1996 Aug 23;261(3):322-7
references.pmid: 8780774
references.citation: Mutat Res. 1997 Sep;382(1-2):5-11
references.pmid: 9360633