Which transposable elements are active in the human genome?

Trends in Genetics

Volumn 23, Issue 4, 2007, Pages 183-191

  Mills, Ryan E ^a   Bennett, E Andrew ^a   Iskow, Rebecca C ^a   Devine, Scott E ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REPETITIVE DNA;

ALU GENE; BIOINFORMATICS; GENE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN GENOME; LONG INTERSPERSED REPEAT; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; REVIEW; SHORT INTERSPERSED REPEAT; TRANSPOSON; VARIABLE NUMBER OF TANDEM REPEAT;

BASE PAIRING; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 33947705203     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2007.02.006     Document Type: Review

References (96)

1. In: Craig N.L., et al. (Ed). Mobile DNA II (2002), ASM Press
2. Batzer M.A., and Deininger P.L. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3 (2002) 370-379
3. Ostertag E.M., and Kazazian Jr. H.H. Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35 (2001) 501-538
4. Chen J.M., et al. Meta-analysis of gross insertions causing human genetic disease, novel mutational mechanisms and the role of replication slippage. Hum. Mutat. 25 (2005) 207-221
5. Cordaux R., et al. Estimating the retrotransposition rate of human Alu elements. Gene 373 (2006) 134-137
6. Li X., et al. Frequency of recent retrotransposition events in the human factor IX gene. Hum. Mutat. 17 (2001) 511-519
7. Kazazian H.H. An estimated frequency of endogenous insertional mutations in humans. Nat. Genet. 22 (1999) 130
8. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
9. Kent W.J., et al. The human genome browser at UCSC. Genome Res. 12 (2002) 996-1006
10. Jurka J. Repbase update a database and an electronic journal of repetitive elements. Trends Genet. 16 (2000) 418-420
11. Smit A.F.A., and Riggs A.D. Tiggers and other DNA transposon fossils in the human genome. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 1443-1448
12. Britten R.J., and Kohn D.E. Repeated sequences in DNA. Science 161 (1968) 529-540
13. Wallace M.R., et al. A de novo Alu insertion results in neurofibromatosis type 1. Nature 353 (1991) 864-866
14. Kazazian Jr. H.H., et al. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332 (1988) 164-166
15. Skowronski J., et al. Unit length Line-1 transcripts in human teratocarcinoma cells. Mol. Cell. Biol. 8 (1988) 1384-1397
16. Mathias S.L., et al. Reverse transcriptase encoded by a human transposable element. Science 254 (1991) 1808-1810
17. Hedges D.J., et al. Differential Alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Res. 14 (2004) 1068-1075
18. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (2005) 69-87
19. Mills R.E., et al. Recently mobilized transposons in the human and chimpanzee genomes. Am. J. Hum. Genet. 78 (2006) 671-679
20. Bennett E.A., et al. Natural genetic variation caused by transposable elements in humans. Genetics 168 (2004) 933-951
21. Wang J., et al. Whole genome computational comparative genomics, a fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365 (2006) 11-20
22. Watanabe H., et al. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429 (2004) 382-388
23. Carroll M.L., et al. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J. Mol. Biol. 311 (2001) 17-40
24. Batzer M.A., et al. Genetic variation of recent Alu insertions in human populations. J. Mol. Evol. 42 (1996) 22-29
25. Salem A.H., et al. Recently integrated Alu elements and human genomic diversity. Mol. Biol. Evol. 20 (2003) 1349-1361
26. Badge R.M., et al. ATLAS: A system to selectively identify human-specific L1 insertions. Am. J. Hum. Genet. 72 (2003) 823-838
27. Myers J.S., et al. A comprehensive analysis of recently integrated human Ta L1 elements. Am. J. Hum. Genet. 71 (2002) 312-326
28. Moran J.V., et al. High frequency retrotransposition in cultured mammalian cells. Cell 87 (1996) 917-927
29. Brouha B., et al. Hot L1s account for the bulk of retrotransposition in the human population. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 5280-5285
30. Lutz S.M., et al. Allelic heterogeneity in LINE-1 retrotransposition activity. Am. J. Hum. Genet. 73 (2003) 1431-1437
31. Seleme Mdel C., et al. Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 6611-6616
32. Dewannieux M., et al. LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35 (2003) 41-48
33. Boeke J.D. LINEs and Alus - the polyA connection. Nat. Genet. 16 (1997) 6-7
34. Sarrowa J., et al. The decline in human Alu retroposition was accompanied by an asymmetric decrease in SRP9/14 binding to dimeric Alu RNA and increased expression of small cytoplasmic Alu RNA. Mol. Cell. Biol. 17 (1997) 1144-1151
35. Ostertag E.M., et al. SVA is a nonautonomous retrotransposon that causes diseases in humans. Am. J. Hum. Genet. 73 (2003) 1444-1451
36. Wei W., et al. Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell. Biol. 21 (2001) 1429-1439
37. Boissinot S., et al. L1 (LINE1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17 (2000) 915-928
38. Wang H., et al. SVA elements: a hominid-specific retroposon family. J. Mol. Biol. 354 (2005) 994-1007
39. Ivics Z., et al. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91 (1997) 501-510
40. Miskey C., et al. The Frog Prince: a reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells. Nucleic Acids Res. 31 (2003) 6873-6881
41. Dewannieux M., et al. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res. 16 (2006) 1548-1556
42. Brodsky I., et al. Expression of HERV-K proviruses in human leukocytes. Blood 81 (1993) 2369-2374
43. Hasler J., and Strub K. Alu elements as regulators of gene expression. Nucleic Acids Res. 34 (2006) 5491-5497
44. Wang J., et al. dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans. Hum. Mutat. 27 (2006) 323-329
45. Teugels E., et al. De novo Alu element insertions targeted to a sequence common to the BRCA1 and BRCA2 genes. Hum. Mutat. 26 (2005) 284
46. Kloor M., et al. A large MSH2 Alu insertion mutation causes HNPCC in a German kindred. Hum. Genet. 115 (2004) 432-438
47. Janicic N., et al. Insertion of an Alu sequence in the Ca(2+)-sensing receptor gene in familial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism. Am. J. Hum. Genet. 56 (1995) 880-886
48. Arcot S.S., et al. Identification and characterization of two polymorphic Ya5 Alu repeats. Mutat. Res. 382 (1997) 5-11
49. Watkins W.S., et al. Patterns of ancestral human diversity, an analysis of Alu-insertion and restriction-site polymorphisms. Am. J. Hum. Genet. 68 (2001) 738-752
50. Otieno A.C., et al. Analysis of the human Alu Ya-lineage. J. Mol. Biol. 342 (2004) 109-118
51. Mamedov I.Z., et al. Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Res. 33 (2005) e16
52. Roy A.M., et al. Potential gene conversion and source genes for recently integrated Alu elements. Genome Res. 10 (2000) 1485-1495
53. Economou-Pachnis A., and Tsichlis P.N. Insertion of an Alu SINE in the human homologue of the Mlvi-2 locus. Nucleic Acids Res. 13 (1985) 8379-8387
54. Abdelhak S., et al. Clustering of mutations responsible for branchio-oto-renal BOR syndrome in the eyes absent homologous region eyaHR of EYA1. Hum. Mol. Genet. 16 (1997) 2247-2255
55. Claverie-Martin F., et al. De novo insertion of an Alu sequence in the coding region of the CLCN5 gene results in Dent's disease. Hum. Genet. 113 (2003) 480-485
56. Ishihara N., et al. Clinical and molecular analysis of Mowat-Wilson syndrome associated with ZFHX1B mutations and deletions at 2q22-q24.1. J. Med. Genet. 41 (2004) 387-393
57. Mustajoki S., et al. Insertion of Alu element responsible for acute intermittent porphyria. Hum. Mutat. 13 (1999) 431-438
58. Oldridge M., et al. De novo alu-element insertions in FGFR2 identify a distinct pathological basis for Apert syndrome. Am. J. Hum. Genet. 64 (1999) 446-461
59. Tighe P.J., et al. Inactivation of the Fas gene by Alu insertion, retrotransposition in an intron causing splicing variation and autoimmune lymphoproliferative syndrome. Genes Immun. 3 Suppl. 1 (2002) S66-S70
60. Vidaud D., et al. Haemophilia B due to a de novo insertion of a human-specific Alu subfamily member within the coding region of the factor IX gene. Eur. J. Hum. Genet. 1 (1993) 30-36
61. Wulff K., et al. Identification of a novel large F9 gene mutation-an insertion of an Alu repeated DNA element in exon e of the factor 9 gene. Hum. Mutat. 15 (2000) 299
62. Batzer M.A., et al. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J. Mol. Biol. 247 (1995) 418-427
63. Carter A.B., et al. Genome-wide analysis of the human Alu Yb-lineage. Hum. Genomics 1 (2004) 167-178
64. Callinan P.A., et al. Comprehensive analysis of Alu-associated diversity on the human sex chromosomes. Gene 317 (2003) 103-110
65. Halling K.C., et al. Hereditary desmoid disease in a family with a germline Alu I repeat mutation of the APC gene. Hum. Hered. 49 (1999) 97-102
66. Sukarova E., et al. An Alu insert as the cause of a severe form of hemophilia A. Acta Haematol. 106 (2001) 126-129
67. Sobrier M.L., et al. Alu-element insertion in the homeodomain of HESX1 and aplasia of the anterior pituitary. Hum. Mutat. 25 (2005) 503
68. Ganguly A., et al. Exon skipping caused by an intronic insertion of a young Alu Yb9 element leads to severe hemophilia A. Hum. Genet. 113 (2003) 348-352
69. Muratani K., et al. Inactivation of the cholinesterase gene by Alu insertion, possible mechanism for human gene transposition. Proc. Natl. Acad. Sci. U. S. A. 88 (1991) 11315-11319
70. Kutsche K., et al. Characterization of breakpoint sequences of five rearrangements in L1CAM and ABCD1 (ALD) genes. Hum. Mutat. 19 (2002) 526-535
71. Su L.K., et al. Genomic rearrangements of the APC tumor-suppressor gene in familial adenomatous polyposis. Hum. Genet. 106 (2000) 101-107
72. Garber R.K., et al. The Alu Yc1 subfamily: sorting the wheat from the chaff. Cytogenet. Genome Res. 110 (2005) 537-542
73. Conley M.E., et al. Two independent retrotransposon insertions at the same site within the coding region of BTK. Hum. Mutat. 25 (2005) 324-325
74. Miki Y., et al. Mutation analysis in the BRCA2 gene in primary breast cancers. Nat. Genet. 13 (1996) 245-247
75. Stoppa-Lyonnet D., et al. Clusters of intragenic Alu repeats predispose the human C1 inhibitor locus to deleterious rearrangements. Proc. Natl. Acad. Sci. U. S. A. 87 (1990) 1551-1555
76. Zhang Y., et al. AluY insertion (IVS4-52ins316alu) in the glycerol kinase gene from an individual with benign glycerol kinase deficiency. Hum. Mutat. 15 (2000) 316-323
77. Xing J., et al. Comprehensive analysis of two Alu Yd subfamilies. J. Mol. Evol. 57 Suppl. 1 (2003) S76-S89
78. Park E.S., et al. Analysis of newly identified low copy AluYj subfamily. Genes Genet. Syst. 80 (2005) 415-422
79. Narita N., et al. 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 (1993) 1862-1867
80. Martinez-Garay I., et al. Intronic L1 insertion and F268S, novel mutations in RPS6KA3 (RSK2) causing Coffin-Lowry syndrome. Clin. Genet. 64 (2003) 491-496
81. Holmes S.E., et al. A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nat. Genet. 7 (1994) 143-148
82. Mukherjee S., et al. Molecular pathology of haemophilia B, identification of five novel mutations including a LINE 1 insertion in Indian patients. Haemophilia 10 (2004) 259-263
83. van den Hurk J.A., et al. Novel types of mutation in the choroideremia (CHM) gene, a full-length L1 insertion and an intronic mutation activating a cryptic exon. Hum. Genet. 113 (2003) 268-275
84. Kondo-Iida E., et al. Novel mutations and genotype-phenotype relationships in 107 families with Fukuyama-type congenital muscular dystrophy (FCMD). Hum. Mol. Genet. 8 (1999) 2303-2309
85. Miki Y., et al. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 52 (1992) 643-645
86. Meischl C., et al. A new exon created by intronic insertion of a rearranged LINE-1 element as the cause of chronic granulomatous disease. Eur. J. Hum. Genet. 8 (2000) 697-703
87. Yoshida K., et al. Insertional mutation by transposable element, L1, in the DMD gene results in X-linked dilated cardiomyopathy. Hum. Mol. Genet. 7 (1998) 1129-1132
88. Divoky V., et al. A novel mechanism of beta-thalassemia. The insertion of L1 retrotransposable element into beta globin IVSII. Blood 88 (1996) 148a
89. Brouha B., et al. Evidence consistent with human L1 retrotransposition in maternal meiosis I. Am. J. Hum. Genet. 71 (2002) 327-336
90. Schwahn U., et al. Positional cloning of the gene for X-linked retinitis pigmentosa 2. Nat. Genet. 19 (1998) 327-332
91. Hassoun H., et al. A novel mobile element inserted in the alpha spectrin gene, spectrin Dayton. A truncated alpha spectrin associated with hereditary elliptocytosis. J. Clin. Invest. 94 (1994) 643-648
92. Kobayashi K., et al. Founder-haplotype analysis in Fukuyama-type congenital muscular dystrophy (FCMD). Hum. Genet. 103 (1998) 323-327
93. Wilund K.R., et al. Molecular mechanisms of autosomal recessive hypercholesterolemia. Hum. Mol. Genet. 11 (2002) 3019-3030
94. Rohrer J., et al. Unusual mutations in Btk, an insertion, a duplication, an inversion, and four large deletions. Clin. Immunol. 90 (1999) 28-37
95. Kobayashi K., et al. An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy. Nature 394 (1998) 388-392
96. Belshaw R., et al. Genomewide screening reveals high levels of insertional polymorphisms in the Human Endogenous Retrovirus Family HERV-K (HML-2): implications for present-day activity. J. Virol. 79 (2005) 12507-12514