Alu retrotransposition-mediated deletion

Journal of Molecular Biology

Volumn 348, Issue 4, 2005, Pages 791-800

  Callinan, Pauline A ^a   Wang, Jianxin ^b   Herke, Scott W ^a   Garber, Randall K ^a   Liang, Ping ^b   Batzer, Mark A ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

^b ROSWELL PARK CANCER INSTITUTE   (United States)

Author keywords

Short interspersed elements; target primed reverse transcription

Indexed keywords

ALU SEQUENCE; ARTICLE; DATA ANALYSIS; DNA RETROTRANSPOSITION; DNA STRAND BREAKAGE; DNA TRANSPOSITION; EVOLUTION; GENE DELETION; GENE LOCUS; GENETIC STABILITY; GENOME; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION;

EID: 17444413395     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.02.043     Document Type: Article

References (39)

1. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome Nature 409 2001 860 921
2. D. Sinnett, C. Richer, J.M. Deragon, and D. Labuda Alu RNA transcripts in human embryonal carcinoma cells. Model of post-transcriptional selection of master sequences J. Mol. Biol. 226 1992 689 706
3. J.D. Boeke LINEs and Alus - the polyA connection Nature Genet. 16 1997 6 7
4. M. Dewannieux, C. Esnault, and T. Heidmann LINE-mediated retrotransposition of marked Alu sequences Nature Genet. 35 2003 41 48
5. P.L. Deininger, M.A. Batzer, C.A. Hutchison III, and M.H. Edgell Master genes in mammalian repetitive DNA amplification Trends Genet. 8 1992 307 311
6. P.L. Deininger, and M.A. Batzer Alu repeats and human disease Mol. Genet. Metab. 67 1999 183 193
7. M.A. Batzer, and P.L. Deininger Alu repeats and human genomic diversity Nature Rev. Genet. 3 2002 370 379
8. P.A. Callinan, D.J. Hedges, A.H. Salem, J. Xing, J.A. Walker, and R.K. Garber Comprehensive analysis of Alu-associated diversity on the human sex chromosomes Gene 317 2003 103 110
9. M.L. Carroll, A.M. Roy-Engel, S.V. Nguyen, A.H. Salem, E. Vogel, and B. Vincent Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity J. Mol. Biol. 311 2001 17 40
10. 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. 14 2004 1068 1075
11. J. Xing, A.H. Salem, D.J. Hedges, G.E. Kilroy, W.S. Watkins, and J.E. Schienman Comprehensive analysis of two Alu Yd subfamilies J. Mol. Evol. 57 2003 S76 S89
12. A.C. Otieno, A.B. Carter, D.J. Hedges, J.A. Walker, D.A. Ray, and R.K. Garber Analysis of the human Alu Ya-lineage J. Mol. Biol. 342 2004 109 118
13. A.B. Carter, A.-H. Salem, D.J. Hedges, C. Nguyen Keegan, B. Kimball, and J.A. Walker Genome wide analysis of the human Yb lineage Hum. Genomics 1 2004 167 168
14. J.A. Bailey, G. Liu, and E.E. Eichler An Alu transposition model for the origin and expansion of human segmental duplications Am. J. Hum. Genet. 73 2003 823 834
15. J. Sebat, B. Lakshmi, J. Troge, J. Alexander, J. Young, and P. Lundin Large-scale copy number polymorphism in the human genome Science 305 2004 525 528
16. A.J. Iafrate, L. Feuk, M.N. Rivera, M.L. Listewnik, P.K. Donahoe, and Y. Qi Detection of large-scale variation in the human genome Nature Genet. 36 2004 949 951
17. S.J. Chen, Z. Chen, M.P. Font, L. d'Auriol, C.J. Larsen, and R. Berger Structural alterations of the BCR and ABL genes in Ph1 positive acute leukemias with rearrangements in the BCR gene first intron: further evidence implicating Alu sequences in the chromosome translocation Nucl. Acids Res. 17 1989 7631 7642
18. N. McNeil Alu elements: repetitive DNA as facilitators of chromosomal rearrangement J. Assoc. Genet. Technol. 30 2004 41 47
19. T. Hayakawa, Y. Satta, P. Gagneux, A. Varki, and N. Takahata Alu-mediated inactivation of the human CMP- N-acetylneuraminic acid hydroxylase gene Proc. Natl Acad. Sci. USA 98 2001 11399 11404
20. A.H. Salem, G.E. Kilroy, W.S. Watkins, L.B. Jorde, and M.A. Batzer Recently integrated Alu elements and human genomic diversity Mol. Biol. Evol. 20 2003 1349 1361
21. N. Gilbert, S. Lutz-Prigge, and J.V. Moran Genomic deletions created upon LINE-1 retrotransposition Cell 110 2002 315 325
22. D.E. Symer, C. Connelly, S.T. Szak, E.M. Caputo, G.J. Cost, G. Parmigiani, and J.D. Boeke Human l1 retrotransposition is associated with genetic instability in vivo Cell 110 2002 327 338
23. T.A. Morrish, N. Gilbert, J.S. Myers, B.J. Vincent, T.D. Stamato, and G.E. Taccioli DNA repair mediated by endonuclease-independent LINE-1 retrotransposition Nature Genet. 31 2002 159 165
24. A.M. Roy-Engel, M.L. Carroll, E. Vogel, R.K. Garber, S.V. Nguyen, and A.H. Salem Alu insertion polymorphisms for the study of human genomic diversity Genetics 159 2001 279 290
25. K. Han, and J. Xing Extended retrotranspositonal quiescence supports a back seat driver model of Alu evolution Genome Res. 2005 In the press
26. N. Yu, M.I. Jensen-Seaman, L. Chemnick, J.R. Kidd, A.S. Deinard, and O. Ryder Low nucleotide diversity in chimpanzees and bonobos Genetics 164 2003 1511 1518
27. A. Fischer, V. Wiebe, S. Paabo, and M. Przeworski Evidence for a complex demographic history of chimpanzees Mol. Biol. Evol. 21 2004 799 808
28. J.M. Bishop, and H. Varmus Functions and origins of retroviral oncogenes R. Weiss N. Teich H. Varmus J. Coffin Molecular Biology of the Tumor Viruses: RNA Tumor Viruses 1982 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY 999 1108
29. R.K. Garber, D.J. Hedges, S.W. Herke, N.W. Hazard, and M.A. Batzer The Alu Yc1 subfamily: sorting the wheat from the chaff Cytogenet. Genome Res. 2005 In the press
30. G. Liu, S. Zhao, J.A. Bailey, S.C. Sahinalp, C. Alkan, E. Tuzun, E.D. Green, and E.E. Eichler Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome Genome Res. 13 2003 358 368
31. H.H. Kazazian Jr, and J.L. Goodier LINE drive. retrotransposition and genome instability Cell 110 2002 277 280
32. I. Ovchinnikov, A.B. Troxel, and G.D. Swergold Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion Genome Res. 11 2001 2050 2058
33. S. Chambeyron, A. Bucheton, and I. Busseau Tandem UAA repeats at the 3′-end of the transcript are essential for the precise initiation of reverse transcription of the I factor in Drosophila melanogaster J. Biol. Chem. 277 2002 17877 17882
34. D.D. Luan, and T.H. Eickbush RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element Mol. Cell. Biol. 15 1995 3882 3891
35. P.L. Deininger, and M.A. Batzer Evolution of retroposons Evolut. Biol. 27 1993 157 196
36. A.M. Roy, M.L. Carroll, D.H. Kass, S.V. Nguyen, A.H. Salem, M.A. Batzer, and P.L. Deininger Recently integrated human Alu repeats: finding needles in the haystack Genetica 107 1999 149 161
37. W.J. Kent BLAT - the BLAST-like alignment tool Genome Res. 12 2002 656 664
38. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
39. F. Sanger, S. Nicklen, and A.R. Coulson DNA sequencing with chain-terminating inhibitors Proc. Natl Acad. Sci. USA 74 1977 5463 5467