Sectorial mutagenesis by transposable elements

Genetica

Volumn 107, Issue 1-3, 1999, Pages 239-248

  Jurka, Jerzy ^a   Kapitonov, Vladimir V ^a  

^a Genetic Information Research Institute   (United States)

Author keywords

Chromosomal evolution; Mutagenesis; Repetitive DNA; Transposable elements

Indexed keywords

EUKARYOTA;

DNA;

ARTICLE; CHROMOSOME; GENETICS; MOLECULAR GENETICS; MUTAGENESIS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY; TRANSPOSON;

BASE SEQUENCE; CHROMOSOMES; DNA; DNA TRANSPOSABLE ELEMENTS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; PHYLOGENY; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 0033287225     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1003989620068     Document Type: Article

References (77)

1. Agrawal, A., Q.M. Eastman & D.G. Schatz, 1998. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394: 744-751.
2. Bernardi, G., 1989. The isochore organization of the human genome. Annu. Rev. Genet. 23: 637-661.
3. Bernardi, G., 1995. The human genome: organization and evolutionary history. Annu. Rev. Genet. 29: 445-476.
4. Bird, A., 1997. Does DNA methylation control transposition of selfish elements in germline? Trends Genet. 13: 469-470.
5. Boyle, A.L., S.G. Ballard & D.C. Ward, 1990. Differential distribution of long and short interspersed element sequences in the mouse genome: chromosome karyotyping by fluorescence in situ hybridization. Proc. Natl. Acad. Sci. USA 87: 7757-7761.
6. Britten, R.J., W.F. Baron, D.B. Stout & E.H. Davidson, 1988, Sources and evolution of human Alu repeated sequences. Proc. Natl. Acad. Sci. USA 85: 4770-4774.
7. Chen, T.L. & L. Manuelidis, 1989. SINEs and LINEs cluster in distinct DNA fragments of Giemsa band size. Chromosoma 98: 309-316.
8. Cherry, S.R. & D. Baltimore, 1999. Chromatin remodeling directly activates V(D)J recombination. Proc. Natl. Acad. Sci. USA 96: 10788-10793.
9. Craig, J.M. & W.A. Bickmore, 1997. The relationship between gene density and chromosome banding patterns in mammalian nuclei, pp. 65-83 in Chromosomes Today, edited by N. Henriques-Gil, J. S. Parker and M. J. Puertas. Chapman & Hall, London, UK.
10. de Souza, S.J., M. Long, R.J. Klein, S. Roy, S. Lin et al., 1998. Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc. Natl. Acad. Sci. USA 95: 5094-5099.
11. Deininger, R.L. & M.A. Batzer, 1999 Alu repeats and human disease. Mol. Genet. Metab. 67: 183-193.
12. Dhellin, O., J. Maestre & T. Heidmann, 1997. Functional differences between the human LINE retrotransposon and retroviral reverse transcriptases for in vivo reverse transcription. EMBO J. 16: 6590-6602.
13. Dimitri, P., 1997. Constitutive heterochromatin and transposable elements in Drosophila melanogaster. Genetica 100: 85-93.
14. Donovan, G.P., C. Harden, J. Gal, L. Ho, E. Sibille et al., 1997. Sensitivity to jerky gene dosage underlies epileptic seizures in mice. J. Neurosci. 17: 4562-4569.
15. Doolittle, W.F. & C. Sapienza, 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.
16. Duret, L., D. Mouchiroud & C. Gautier, 1995. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40: 308-317.
17. Halverson, D., M. Baum, J. Stryker, J. Carbon & L. Clarke, 1997. A centromere DNA-binding protein from fission yeast affects chromosome segregation and has homology to human CENP-B. J. Cell Biol. 136: 487-500.
18. Hartl, D.L., E.R. Lozovskaya, D.I. Nurminsky & A.R. Lohe, 1997. What restricts the activity of mariner-like transposable elements? Trends Genet. 13: 197-201.
19. Hiom, K., M. Melek & M. Gellert, 1998. DNA transposition by the RAG1 and RAG2 proteins: A possible source of oncogenic translocations. Cell 94: 463-470.
20. Holmquist, G.P., 1992. Chromosome bands, their chromatin flavors, and their functional features. Am. J. Hum. Genet. 51: 17-37.
21. Hu, X. & R.G. Worton, 1992. Partial gene duplication as a cause of human disease. Hum. Mutat. 1: 3-12.
22. Jabbari, K. & G. Bernardi, 1998. CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families. Gene 224: 123-128.
23. Jackson, D.A., 1997. Chromatin domains and nuclear compartments: establishing sites of gene expression in eukaryotic nuclei. Mol. Biol. Rep. 24: 209-220.
24. Jensen, S., M.P. Gassama & T. Heidmann, 1999. Taming of transposable elements by homology-dependent gene silencing. Nat. Genet. 21: 209-212.
25. Jurka, J., 1989. Subfamily structure and evolution of the human L1 family of repetitive sequences. J. Mol. Evol. 29: 496-503.
26. Jurka, J., 1995. Origin and evolution of Alu repetitive elements, pp. 25-41 in The Impact of Short Interspersed Elements (SINEs) on the Host genome, edited by R.J. Maraia. R.G. Landes Company, Austin.
27. Jurka, J., 1997 Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94: 1872-1877.
28. Jurka, J., 1998. Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 8: 333-337.
29. Jurka, J. & A. Milosavljevic, 1991, Reconstruction and analysis of human Alu genes. J. Mol. Evol. 32: 105-121.
30. Jurka, J. & T. Smith, 1988. A fundamental division in the Alu family of repeated sequences. Proc. Natl. Acad. Sci. USA 85: 4775-4778.
31. Jurka, J., E. Zietkiewicz & D. Labuda, 1995. Ubiquitous mammalian interspersed repeats (MIRs) are molecular fossils from the Mesozoic era. Nucl. Acids Res. 23: 170-175.
32. Jurka, J., V.V. Kapitonov, P. Klonowski, J. Walichiewicz & A.F.A. Smit, 1996. Identification of new medium reiteration frequency repeats in the genomes of primates, rodentia and lagomorpha. Genetica 98: 235-247.
33. Kapitonov, V.V. & J. Jurka, 1996 The age of Alu subfamilies. J. Mol. Evol. 42: 59-65.
34. Kapitonov, V. & J. Jurka, 1998. MER53, a non-autonomous DNA transposon associated with a variety of functionally related defense genes in the human genome. DNA Sequence 8: 277-288.
35. Kaplan, N., T. Darden & C.H. Langley, 1985. Evolution and extinction of transposable elements in Mendelian populations. Genetics 109: 459-480.
36. Kazazian, H.H. Jr. & J.V. Moran, 1998. The impact of L1 retrotransposons on the human genome. Nat. Genet. 19: 19-24.
37. Kidwell, M.G. & D. Lisch, 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 94: 7704-7711.
38. Kipling, D. & P.E. Warburton, 1997. Centromeres, CENP-B and Tigger too. Trends Genet. 13: 141-145.
39. Korenberg, J.R. & M.C. Rykowski, 1988. Human genome organization: Alu, Lines and the molecular structure of metaphase chromosome bands. Cell 53: 391-400.
40. Kumar, S., K. Tamamura & M. Nei, 1994. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput. Appl. Biosci. 10: 189-191.
41. Labrador, M. & V.G. Corces, 1997. Transposable element-host interactions: regulation of insertion and excision. Ann. Rev. Biochem. 31: 381-404.
42. Lewis, S.M., 1999. Evolution of immunoglobulin and T-cell receptor gene assembly. Ann. N Y Acad. Sci. 870: 58-67.
43. Ligner, J., T.R. Hughes, A. Shevchenko, M. Mann, V. Lundblad et al., 1997. Reverse transcriptase motifs in the catalytic subunit of telomerase. Science 276: 561-567.
44. Logsdon, J.M., Jr. & J.D. Palmer, 1994. Origin of introns - early or late? Nature 369: 526.
45. Malick, H.S., W.D. Burke & T.H. Eickbush, 1999. The age and evolution of non-LTR retrotranposable elements. Mol. Biol. Evol. 16: 793-805.
46. Manuelidis, L. & D.C. Ward, 1984. Chromosomal and nuclear distribution of the 1.9-kb human DNA repeat segment. Chromosoma 91: 28-38.
47. Matassi, G., D. Labuda & G. Bernardi, 1998. Distribution of mammalian-wide interspersed repeats (MIRs) in the isochores of the human genome. FEBS Lett. 439: 63-65.
48. Matzke, M.A. & A.J. Matzke, 1998. Epigenetic silencing of plant transgenes as a consequence of diverse cellular defence responses. Cell. Mol. Life Sci. 54: 94-103.
49. McDonald, J.F., 1993. Evolution and consequences of transposable elements. Curr. Opin. Genet. Dev. 3: 855-864.
50. McDonald, J.F., 1995. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10: 123-126.
51. Miki, Y., 1998. Retrotransposal integration of mobile genetic elements in human diseases. J. Hum. Genet. 43: 77-84.
52. Nakamura, T.M., B.M. Gregg, K.B. Chapman, S.L. Weinrich, W.H. Andrews et al., 1997. Telomerase catalytic subunit homologs from fission yeast and human. Science 277: 955-959.
53. Okada, N., M. Hamada, I. Ogiwara & K. Ohshima, 1997. SINEs and LINEs share common 3′ sequences: a review. Gene 205: 229-243.
54. Orgel, L.E. & F.H.C. Crick, 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607.
55. Pardue, M.L., O.N. Danilevskaya, K.L. Traverse & K. Lowenhaupt, 1997. Evolutionary links between telomeres and transposable elements. Genetica 100: 73-84.
56. Pirrotta, V. & L. Rastelli, 1994. White gene expression, repressive chromatin domains and homeotic gene regulation in Drosophila. Bioessays 16: 549-556.
57. Robertson, H.M., 1996. Members of pogo superfamily of DNA-mediated transposons in the human genome. Mol. Gen. Genet. 252: 761-766.
58. Roger, A.J., P.J. Keeling & W.F. Doolittle, 1994. Introns, the broken transposons. Soc. Gen. Physiol. Ser. 49: 27-37.
59. Roth, D.B. & N.L. Craig, 1998. VDJ Recombination: A transposase goes to work. Cell 94: 411-414.
60. Schmid, C.W., 1998. Does SINE evolution preclude Alu function? Nucl. Acids Res. 26: 4541-4550.
61. Shapiro, J.A., 1999. Genome system architecture and natural genetic engineering in evolution. Ann. N. Y. Acad. Sci. 870: 23-35.
62. Smit, A.F. A., 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6: 743-748.
63. Smit, A.F.A. & A.D. Riggs, 1996. Tiggers and other DNA transposon fossils in the human genome. Proc. Natl. Acad. Sci. USA 93: 1443-1448.
64. Smit, A.F.A., G. Toth, A.D. Riggs & J. Jurka, 1995. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246: 401-417.
65. Soriano, P., M. Meunier-Rotival & G. Bernardi, 1983. The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes. Proc. Natl. Acad. Sci. USA 80: 1816-1820.
66. Stoltzfus, A., D.F. Spencer, M. Zuker, J.M. Logsdon, Jr. & W.F. Doolittle, 1994. Testing the exon theory of genes:the evidence from protein structure. Science 265: 202-207.
67. Surzycki, S.A. & W.R. Belknap, 2000. Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans chromosomes. Proc. Natl. Acad. Sci. USA 97: 245-249.
68. Szmulewicz, M.N., G.E. Novick & R.J. Herrera, 1998. Effects of Alu insertions on gene function. Electrophoresis 19: 1260-1264.
69. Thompson, J.D., D.G. Higgins & T.J. Gibson, 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
70. Toth, M., J. Grimsby, G. Buzsaki & G.P. Donovan, 1995. Epileptic seizures caused by inactivation of a novel gene, jerky, related to centromere binding protein-B in transgenic mice. Nat. Genet. 11: 71-75.
71. von Sternberg, R.M., G.E. Novick, G.-P. Gao & R.J. Herrera, 1992. Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA. Genetica 86: 215-246.
72. von Sternberg, R., 1996. The role of constrained self-organization in genome structural evolution. Acta Biotheoretica 44: 95-118.
73. Wichman, H.A., R.A. Van den Bussche, M.J. Hamilton & R.J. Baker, 1992. Transposable elements and the evolution of genome organization in mammals. Genetica 86: 287-293.
74. Wilson, R.K. et al., 1999. How the worm was won. The C. elegans genome sequencing project. Trends Genet. 15: 51-58.
75. Woese, C., 1998. The universal ancestor. Proc. Natl. Acad. Sci. USA 95: 6854-6859.
76. Yang, A.S., M.L. Gonzalgo, J.M. Zingg, R.P. Millar, J.D. Buckley et al., 1996. The rate of CpG mutation in Alu repetitive elements within the p53 tumor suppressor gene in the primate germline. J. Mol. Biol. 258: 240-250.
77. Yoder, J.A., C.P. Walsh & T.H. Bestor, 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13: 335-340.