Natural genetic variation caused by transposable elements in humans

Genetics

Volumn 168, Issue 2, 2004, Pages 933-951

  Bennett, E Andrew ^a   Coleman, Laura E ^a   Tsui, Circe ^a   Pittard, W Stephen ^a   Devine, Scott E ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALU SEQUENCE; ARTICLE; GENE DELETION; GENE INSERTION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TRANSPOSON; TRANSPOSON LIKE REPETITIVE ELEMENT;

DNA TRANSPOSABLE ELEMENTS; GENOME, HUMAN; HUMANS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

INSERTION SEQUENCES; TRANSPOSONS;

EID: 8544229065     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.031757     Document Type: Article

References (73)

1. ABDEL-HALIM, S., G. E. KILROY, W. S. WATKINS, L. B. JORDE and M. A. BATZER, 2003 Recently integrated Alu elements and human genomic diversity. Mol. Biol. Evol. 20: 1349-1361.
2. BADGE, R. M., R. S. ALISCH and J. V. MORAN, 2003 ATLAS: a system to selectively identify human-specific L1 insertions. Am. J. Hum. Genet. 72: 823-838.
3. BAILEY, J. A., Z. GU, R. A. CLARK, K. REINERT, R. V. SAMONTE et al., 2002 Recent segmental duplications in the human genome. Science 297: 1003-1007.
4. BATZER, M. A., and P. L. DEININGER, 2002 Alu repeats and human genomic diversity. Nat. Rev. Genet. 3: 370-379.
5. BEDELL, J. A., I. KORF and W. GISH, 2000 MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16: 1040-1041.
6. BERG, D. E., and M. M. HOWE, 1989 Mobile DNA. American Society for Microbiology, Washington, DC.
7. BERGER, J., T. SUZUKI, K. A. SENTI, J. STUBBS, G. SCHAFENER et al., 2001 Genetic mapping with SNP markers in Drosophila. Nat. Genet. 29: 475-481.
8. BOEKE, J. D., 1997 LINEs and Alus - the poly A connection. Nat. Genet. 16: 6-7.
9. BOISSINOT, S., P. CHEVRET and A. FURANO, 2000 L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17: 915-928.
10. BRITTEN, R. J., W. F. BARON, D. STOUT and E. H. DAVIDSON, 1988 Sources and evolution of human Alu repeated sequences. Proc. Natl. Acad. Sci. USA 85: 4770-4774.
11. BROUHA, B., J. SCHSTAK, R. M. BADGE, S. LUTZ-PRIGG, A. H. FARBEY et al., 2003 Hot L1s account for the bulk of retrotransposition in the human population. Proc. Natl. Acad. Sci. USA 100: 5280-5285.
12. CARROLL, M. L., A. M. ROY-ENGEL, S. V. NGUYEN, A. SALEM, E. VOGEL et al., 2001 Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J. Mol. Biol. 311: 17-40.
13. COLLINS, F. S., M. L. DRUMM, J. L. COLE, W. K. LOCKWOOD, G. F. VANDE WOUDE et al., 1987 Construction of a general human chromosome jumping library, with application to cystic fibrosis. Science 235: 1046-1049.
14. COLLINS, F. S., L. D. BROOKS and A. CHAKRAVARTI, 1999 A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8: 1229-1231.
15. COST, G. J., Q. FENG, A. JACQUIER and J. D. BOEKE, 2002 Human L1 element target-primed reverse transcription in vitro. EMBO J. 21: 5899-5910.
16. DEININGER, P. L., and M. A. BATZER, 1999 Alu repeats and human disease. Mol. Genet. Metab. 67: 183-193.
17. DEININGER, P. L., M. A. BATZER, C. A. HUTCHISON and M. H. EDGELL, 1992 Master genes in mammalian repetitive DNA amplification. Trends Genet. 8: 307-311.
18. DEWANNIEUX, M., C. ESNAULT and T. HEIDMANN, 2003 LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35: 41-48.
19. ESNAULT, C., J. MAESTRE and T. HEIDMANN, 2000 Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24: 363-367.
20. EWING, B., and P. GREEN, 1998 Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
21. EWING, B., L. HILLIER, M. C. WENDL and P. GREEN, 1998 Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
22. FENG, Q., J. V. MORAN, H. H. KAZAZIAN and J. D. BOEKE, 1996 Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905-916.
23. HASSOUN, H., T. L. COETZER, J. N. VASSILIADIS, K. E. SAHR, G. J. MAALOUF et al., 1994 A novel mobile element inserted in the alpha spectrin gene. Spectrin Dayton. J. Clin. Invest. 94: 643-648.
24. HOHJOH, H., and M. F. SINGER, 1996 Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA. EMBO J. 15: 630-639.
25. HOHJOH, H., and M. F. SINGER, 1997a Sequence-specific single-strand RNA binding protein encoded by the human LINE-1 retrotransposon. EMBO J. 16: 6034-6043.
26. HOHJOH, H., and M. F. SINGER, 1997b Ribonuclease and high salt sensitivity of the ribonucleoprotein complex formed by the human LINE-1 retrotransposon. J. Mol. Biol. 271: 7-12.
27. INTERNATIONAL HAPMAP CONSORTIUM, 2003 The international HapMap project. Nature 426: 789-796.
28. JOHANNING, K., C. A. STEVENSON, O. O. OYENIRAN, Y. M. GOZAL, A. M. ROY-ENGEL et al., 2003 Potential for retroposition by old Alu subfamilies. J. Mol. Evol. 56: 658-664.
29. JUDSON, R., B. SALISBURY, J. SCHNEIDER, A. WINDEMUTH and J. C. STEPHENS, 2002 How many SNPs does a genome-wide haplotype map require? Pharmacogenomics 3: 379-391.
30. JURKA, J., 2000 Repbase update - a database and an electronic journal of repetitive elements. Trends Genet. 16: 418-420.
31. JURKA, J., M. KRNJAJIC, V. V. KAPITONOV, J. E. STENGER and O. KOKHANYY, 2002 Active Alu elements are passed primarily through paternal germlines. Theor. Popul. Biol. 61: 519-530.
32. JURKA, J., and T. SMITH, 1988 A fundamental division in the Alu family of repeated sequences. Proc. Natl. Acad. Sci. USA 85: 4775-4778.
33. JURKA, J., and E. ZUCKERKANDL, 1991 Free left arms as precursor molecules in the evolution of Alu sequences. J. Mol. Evol. 33: 49-56.
34. KAZAZIAN, H. H., C. WONG, H. YOUSSOUFIAN, A. F. SCOTT, D. G. PHILLIPS et al., 1988 Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism formulation in man. Nature 332: 164-166.
35. KENT, W. J., 2002 BLAT - the BLAST-like alignment tool. Genome Res. 12: 656-664.
36. KENT, W. J., C. W. SUGNET, T. S. FUREY, K. M. ROSKIN, T. H. PRINGLE et al., 2002 The human genome browser at UCSC. Genome Res. 12: 996-1006.
37. KIMMEL, B., M. PALOZZOLO, C. MARTIN, J. D. BOEKE and S. E. DEVINE, 1997 Transposon-mediated DNA sequencing, pp. 455-532 in Genome Analysis: A Laboratory Manual, Vol. 1, edited by B. BIRREN, E. D. GREEN, R. M. MYERS and P. HIETER. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
38. KOBAYASHI, K., Y. NAKAHORI, M. MIYAKE, K. MATSUMURA, E. KONDOLIDA et al., 1998 An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy. Nature 394: 388-392.
39. KOLOSHA, V. O., and S. L. MARTIN, 1997 In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition. Proc. Natl. Acad. Sci. USA 94: 10155-10160.
40. LANDER, E. S., L. M. LINTON, B. BIRREN, C. NUSBAUM, M. C. ZODY et al., 2001 Initial sequencing and analysis of the human genome. Nature 409: 860-921.
41. LIU, J., M. M. NAU, J. ZUCMAN-ROSSI, J. I. POWELL, C. J. ALLEGRA et al., 1997 LINE-1 element insertion at the t(11;22) translocation breakpoint of a desmoplastic small round cell tumor. Genes Chromosomes Cancer 18: 232-239.
42. LUAN, D. D., M. H. KORMAN, J. L. JAKUBCZAK and T. H. EICKBUSH, 1993 Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72: 595-605.
43. MARTIN, S. L., and F. D. BUSHMAN, 2001 Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol. Cell. Biol. 21: 467-475.
44. MARTIN, S. L., J. LI and J. A. WEISZ, 2000 Deletion analysis defines distinct functional domains for protein-protein and nucleic acid interactions in the ORF1 protein of mouse LINE-1. J. Mol. Biol. 304: 11-20.
45. MARTIN, S. L., D. BRANCIFORTE, D. KELLER and D. L. BAIN, 2003 Trimeric structure for an essential protein in L1 retrotransposition. Proc. Natl. Acad. Sci. USA 100: 13815-13820.
46. MATHIAS, S. L., A. F. SCOTT, H. H. KAZAZIAN, J. D. BOEKE and A. GABRIEL, 1991 Reverse transcriptase encoded by a human transposable element. Science 254: 1808-1810.
47. MIKI, Y., I. NISHISHO, A. HORII, Y. MIYOSHI, J. UTSUNOMIYA et al., 1992 Disruption of the APC gene by a retrotransposon insertion of L1 sequence in a colon cancer. Cancer Res. 52: 643-645.
48. MIKI, Y., T. KATAGIRI, F. KASUMI, T. YOSHIMOTO and Y. NAKAMURA, 1996 Mutation analysis in the BRCA2 gene in primary breast cancers. Nat. Genet. 13: 245-247.
49. MORAN, J. V., 1999 Human L1 retrotransposition: insights and peculiarities learned from a cultured cell retrotransposition assay. Genetica 107: 39-51.
50. MORAN, J. V., S. E. HOLMES, T. P. NAAS, R. J. DEBERARDINIS and H. H. KAZAZIAN, 1996 High frequency retrotransposition in cultured mammalian cells. Cell 87: 917-927.
51. MORSE, B., P. G. ROTHBERG, V. J. SOUTH, J. M. SPANDORFER and S. M. ASTRIN, 1988 Insertional mutagenesis of the myc locus by a LINE-1 sequence in human breast carcinoma. Nature 333: 87-90.
52. MORRISH, T. A., N. GILBERT, J. S. MYERS, B. J. VINCENT, T. D. STAMATO et al., 2002 DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat. Genet. 31: 159-165.
53. MYERS, J. S., B. J. VINCENT, H. UDALL, W. S. WATKINS, T. A. MORRISH et al., 2002 A comprehensive analysis of recently integrated human Ta L1 elements. Am. J. Hum. Genet. 71: 312-326.
54. NARITA, N., H. NISHIO, Y. KITOH, Y. ISHIKAWA and R. MINAMI, 1993 Insertion of a 5′ truncated L1 element into the 3′ end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy. J. Clin. Invest. 91: 1862-1867.
55. OSTERTAG, E. M., and H. H. KAZAZIAN, JR., 2001 Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35: 501-538.
56. OSTERTAG, E. M., J. L. GOODIER, Y. ZHANG and H. H. KAZAZIAN, 2003 Nonautonomous retrotransposons that cause disease in humans. Am. J. Hum. Genet. 73: 1444-1451.
57. OVCHINNIKOV, I., A. B. TROXEL and G. D. SWERGOLD, 2001 Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion. Genome Res. 11: 2050-2058.
58. OVCHINNIKOV, I., A. RUBIN and G. D. SWERGOLD, 2002 Tracing the LINEs of human evolution. Proc. Natl. Acad. Sci. USA 99: 10522-10527.
59. ROHRER, J., Y. MINEGISHI, D. RICHTER, J. EGUIGUREN and M. E. CONLEY, 1999 Unusual mutations in Btk: an insertion, a duplication, and four large deletions. Clin. Immunol. 90: 28-37.
60. ROY-ENGEL, A. M., M. L. CARROLL, E. VOGEL, R. K. GARBER, S. V. NGUYEN et al., 2001 Alu insertion polymorphisms for the study of human genomic diversity. Genetics 159: 279-290.
61. ROY-ENGEL, A. M., A. H. SALEM, O. O. OYENIRAN, L. DEININGER, D. J. HEDGES et al., 2003 Active Alu element "A-tails": size does matter. Genome Res. 12: 1333-1344.
62. SACHIDANANDAM, R., D. WEISSMAN, S. C. SCHMIDT, J. M. KAKOL, L. D. STEIN et al., 2001 A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.
63. SHEEN, F. M., S. T. SHERRY, G. M. RISCH, M. ROBICHAUX, I. NASIDZE et al., 2000 Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition. Genome Res. 10: 1496-1508.
64. SHEN, L., L. WU, S. SANLIOGLU, R. CHEN, A. R. MENDOZA et al., 1994 Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and C4B genes in the HLA class III region. J. Biol. Chem. 269: 8466-8476.
65. SLAGEL, V., E. FLEMINGTON, V. TRAINA-DORGE, H. BRADSHAW and P. L. DEININGER, 1987 Clustering and relationships of the Alu family in the human genome. Mol. Biol. Evol. 4: 19-29.
66. SMIT, A. F., 1999 Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9: 657-663.
67. SMIT, A. F. A., and A. D. RIGGS, 1996 Tiggers and other DNA transposon fossils in the human genome. Proc. Natl. Acad. Sci. USA 93: 1443-1448.
68. STRICHMAN-ALMASHANU, L. Z., R. S. LEE, P. O. ONYANGO, E. PERLMAN, F. FLAM et al., 2001 A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. Genome Res. 12: 543-554.
69. TSUI, C., L. E. COLEMAN, J. L. GRIFFITH, E. A. BENNETT, S. G. GOODSON et al., 2003 Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map. Nucleic Acids Res. 31:4910-4916.
70. ULLU, E., and C. TSCHUDI, 1984 Alu sequences are processed 7SL RNA genes. Nature 312: 171-172.
71. WEI, W., N. GILBERT, S. L. OOI, J. F. LAWLER, E. M. OSTERTAG et al., 2001 Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell. Biol. 21: 1429-1439.
72. WICKS, S. R., R. T. YEH, W. R. GISH, R. H. WATERSTON and R. H. A. PLASTERK, 2001 Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat. Genet. 28: 160-164.
73. ZHANG, Y., K. M. DIPPLE, E. VILAIN, B. L. HUANG, G. FINLAYSON et al., 2000 AluY insertion (IVS4-52ins316alu) in the glycerol kinase gene from an individual with benign glycerol kinase deficiency. Hum. Mutat. 15: 316-323.