The Suppressor-mutator element and the evolutionary riddle of transposons

Genes to Cells

Volumn 4, Issue 1, 1999, Pages 11-19

  Fedoroff, Nina V ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTION; GENE CONTROL; GENE DUPLICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC TRANSCRIPTION; MAIZE; METHYLATION; NONHUMAN; PRIORITY JOURNAL; RECOMBINANT GENE; REGULATORY MECHANISM; REVIEW; TRANSPOSON;

ZEA MAYS;

EID: 0033061598     PISSN: 13569597     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2443.1999.00233.x     Document Type: Review

References (99)

1. Andersen, R.P. & Roth, J.R. (1977) Tandem genetic duplications in phage and bacteria. Annu. Rev. Microbiol. 31, 473-505.
2. Assaad, F.F., Tucker, K.L. & Signer, E.R. (1993) Epigenetic repeat-induced gene silencing (RIGS) in Arabidopsis. Plant Mol. Biol. 22, 1067-1085.
3. Banks, J.A., Masson, P. & Fedoroff, N. (1988) Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable element. Genes Dev. 2, 1364-1380.
4. Bennetzen, J.L. & Freeling, M. (1997) The unified grass genome: synergy in synteny. Genome Res. 7, 301-306.
5. Bi, X. & Liu, L.F. (1996a) DNA rearrangement mediated by inverted repeats. Proc. Natl. Acad. Sci. USA 93, 819-823.
6. Bi, X. & Liu, L.F. (1996b) A replicational model for DNA recombination between direct repeats. J. Mol. Biol. 256, 849-858.
7. Brink, R.A. (1958) Paramutation at the R locus in maize. Cold Spring Harbor Symp. Quant. Biol. 23, 379-391.
8. Britten, R.J. (1996) DNA sequence insertion and evolutionary variation in gene regulation. Proc. Natl. Acad. Sci. USA 93, 9374-9377.
9. Britten, R.J. (1997) Mobile elements inserted in the distant past have taken on important functions. Gene 205, 177-182.
10. Cerutti, H., Johnson, A.M., Gillham, N.W. & Boynton, J.E. (1997) Epigenetic silencing of a foreign gene in nuclear transformants of Chlamydomonas. Plant Cell 9, 925-945.
11. Chen, R.Z., Pettersson, U., Beard, C., Jackson-Grusby, L. & Jaenisch, R. (1998) DNA hypomethylation leads to elevated mutation rates. Nature 395, 89-93.
12. Ciotta, C., Ceccotti, S., Aquilina, G., et al (1998) Increased somatic recombination in methylation tolerant human cells with defective DNA mismatch repair. J. Mol. Biol. 276, 705-719.
13. Coe, J. & E. H. (1968) Heritable repression due to paramutation in maize. Science 162, 925.
14. Cooper, D.M., Schimenti, K.J. & Schimenti, J.C. (1998) Factors affecting ectopic gene conversion in mice. Mamm. Genome 9, 355-360.
15. Doolittle, W.F. & Sapienza, C. (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284, 601-603.
16. Dorer, D.R. & Henikoff, S. (1997) Transgene repeat arrays interact with distant heterochromatin and cause silencing in cis and Trans. Genetics 147, 1181-1190.
17. Engels, W.R. (1997) Invasions of P elements. Genetics 145, 11-15.
18. Fedoroff, N. (1989a) Maize transposable elements. In: Mobile DNA (eds M. Howe & D Berg), pp. 375-411. Washington, DC: American Society for Microbiology.
19. Fedoroff, N.V. (1989b) The heritable activation of cryptic Suppressor-mutator elements by an active element. Genetics 121, 591-608.
20. Fedoroff, N. (1996) Epigenetic regulation of the maize Spm transposable element. In: Epigenetic Mechanisms of Gene Regulation (eds V.E.A. Russo, R.A. Martienssen & A.D. Riggs), pp. 575-591. Cold Spring Harbor, New York: Cold Spring, Harbor Laboratory Press.
21. Fedoroff, N. V. & Banks, J.A. (1988) Is the Suppressor-mutator element controlled by a basic developmental regulatory mechanism? Genetics 120, 559-577.
22. Feschenko, V.V. & Lovett, S.T. (1998) Slipped misalignment mechanisms of deletion formation: analysis of deletion endpoints. J. Mol. Biol 276, 559-569.
23. Finnegan, E.J., Genger, R.K., Kovac, K., Peacock, W.J. & Dennis, E.S. (1998) DNA methylation and the promotion of flowering by vernalization. Proc. Natl. Acad. Sci. USA 95, 5824-5829.
24. Finnegan, E.J., Peacock, W.J. & Dennis, E.S. (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. USA 93, 8449-8454.
25. Flavell, R.B. (1994) Inactivation of gene expression in plants as a consequence of specific sequence duplication. Proc. Natl. Acad. Sci. USA 91, 3490-3496.
26. Flavell, R.B., Bennett, M.D, Smith, J.B. & Smith, D.B. (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem. Genet. 12, 257-269.
27. Frey, M., Reinecke, J., Grant, S., Saedler, H. & Gierl, A. (1990) Excision of the En/Spm transposable element of Zea mays requires two element-encoded proteins. EMBO J. 9, 4037-4044.
28. Garrick, D., Fiering, S., Martin, D.I. & Whitelaw, E. (1998) Repeat-induced gene silencing in mammals. Nature Genet. 18, 56-59.
29. Gierl, A., Lutticke, S. & Saedler, H. (1988) TnpA product encoded by the transposable element En-I of Zea mays is a DNA binding protein. EMBO J. 7, 4045-4053.
30. Goldman, A.S. & Lichten, M. (1996) The efficiency of meiotic recombination between dispersed sequences in Saccharomyces cerevisiae depends upon their chromosomal location. Genetics 144, 43-55.
31. Gorbunova, V. & Levy, A.A. (1997) Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions. Nucl. Acids Res. 25, 4650-4657.
32. Henikoff, S. & Matzke, M.A. (1997) Exploring and explaining epigenetic effects. Trends Genet. 13, 293-295.
33. Hershkovitz, M., Gruenbaum, Y., Renbaum, P., Razin, A. & Loyter, A. (1990) Effect of CpG methylation on gene expression in transfected plant protoplasts. Gene 94, 189-193.
34. Hollick, J.B., Dorweiller, J.E. & Chandler, V.L. (1997) Paramutation and related allelic interactions. Trends Genet. 13, 302-308.
35. Holliday, R. & Ho, T. (1995) Evidence for gene silencing by DNA methylation in normal human diploid fibroblasts. Somat. Cell Mol. Genet. 21, 215-218.
36. Howe, M. & Berg, D., eds (1989) Mobile DNA. Washington: American Society for Microbiology.
37. Jaenisch, R. (1997) DNA methylation and imprinting: why bother? Trends Genet. 13, 323-329.
38. Jensen, S., Cavarec, L., Gassama, M.P. & Heidmann, T. (1995) Defective I elements introduced into Drosophila as transgenes can regulate reactivity and prevent I-R hybrid dysgenesis. Mol. Gen. Genet. 248, 381-390.
39. Kidwell, M.G. & Lisch, D (1997) Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 94, 7704-7711.
40. Kim, J.M., Vangui, S., Boeke, J.D., Gabriel, A. & Voytas, D.F. (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8, 464-478.
41. Koch, A.L. (1971) The adaptive responses of Escherichia coli to a feast or famine existence. Adv. Microbial Physiol. 6, 147-217.
42. Koch, A.L. (1979) Selection and recombination in populations containing tandem multiple genes. J. Mol. Evol 14, 273-285.
43. Kricker, M.C., Drake, J.W. & Radman, M. (1992) Duplication-targeted DNA methylation and mutagenesis in the evolution of eukaryotic chromosomes. Proc. Natl. Acad. Sci. USA 89, 1075-1079.
44. Kupiec, M. & Petes, T.D. (1988) Allelic and ectopic recombination between Ty elements in yeast. Genetics 119, 549-559.
45. Liang, E, Han, M., Romanienko, P.J. & Jasin, M. (1998) Homology-directed repair is a major double-strand break repair pathway in mammalian cells. Proc. Natl. Acad. Sci. USA 95, 5172-5177.
46. Lichten, M., Borts, R.H. & Haber, J.E. (1987) Meiotic gene conversion and crossing over between dispersed homologous sequences occurs frequently in Saccharomyces cerevisiae. Genetics 115, 233-246.
47. Maloisel, L. & Rossignol, J.L. (1998) Suppression of crossing-over by DNA methylation in Ascobolus. Genes Dev. 12, 1381-1389.
48. Martienssen, R.A. (1996) Epigenetic silencing of Mu transposable elements in maize. In: Epigenetic Mechanisms of Gene Regulation (eds V.E.A. Russo, R.A. Martienssen & A.D. Riggs), pp. 593-608. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
49. Masson, P. & Fedoroff, N.V. (1989) Mobility of the maize Suppressor-tnutator element in transgenic tobacco cells. Proc. Natl. Acad. Sci. USA 86, 2219-2223.
50. Masson, P., Rutherford, G., Banks, J.A. & Fedoroff, N. (1989) Essential large transcripts of the maize Spm element are generated by alternative splicing. Cell 58, 755-765.
51. Masson, P., Surosky, R., Kingsbury, J. & Fedoroff, N.V. (1987) Genetic and molecular analysis of the Spm-dependent a-m2 alleles of the maize a locus. Genetics 117, 117-137.
52. McClintock, B. (1946) Maize genetics. Carnegie Inst. Wash. Yr. Bk. 45, 176-186.
53. McClintock, B. (1950a) Mutable loci in maize. Carnegie Inst. Wash. Yr. Bk. 49, 157-167.
54. McClintock, B. (1950b) The origin and behavior of mutable loci in maize. Proc. Natl. Acad. Sci. USA 36, 344-355.
55. McClintock, B. (1951) Mutable loci in maize. Carnegie Inst. Wash. Yr. Bk. 50, 174-181.
56. McClintock, B. (1957) Genetic and cytological studies of maize. Carnegie Inst. Wash. Yr. Bk. 56, 393-401.
57. McClintock, B. (1958) The suppressor-mutator system of control of gene action in maize. Carnegie Inst. Wash. Yr. Bk. 57, 415-429.
58. McClintock, B. (1959) Genetic and cytological studies of maize. Carnegie Inst. Wash. Yr. Bk. 58, 452-456.
59. McClintock, B. (1961) Further studies of the suppressor-mutator system of control of gene action in maize. Carnegie Inst. Wash. Yr. Bk. Bk 60, 469-476.
60. McClintock, B. (1962) Topographical relations between elements of control systems in maize. Carnegie Inst. Wash. Yr. Bk. Bk 61, 448-461.
61. McClintock, B. (1965) The control of gene action in maize. Brookhaven Symp. Biol. 18, 162-184.
62. McClintock, B. (1971) The contribution of one component of a control system to versatility of gene expression. Carnegie Inst. Wash. Yr. Bk. 70, 5-17.
63. Meyer, P. (1996) Repeat-induced gene silencing: common mechanisms in plants and fungi. Biol. Chem. Hoppe Seyler 377, 87-95.
64. Nyce, J. (1991) Gene silencing in mammalian cells by direct incorporation of electroporated 5-methyl-2′-deoxycytidine 5′-triphosphate. Somat. Cell Mol. Genet. 17, 543-550.
65. Orgel, L.E. & Crick, F.H.C. (1980) Selfish DNA: the ultimate parasite. Nature 284, 604-607.
66. Paszkowski, J., ed. (1994) Homologous Recombination and Gene Silencing in Plants. Boston, MA: Kluwer Academic Publishers.
67. Pereira, A., Cuypers, H., Gierl, A., Schwarz-Sommer, Z. & Saedler, H. (1986) Molecular analysis of the En/Spm transposable element system of Zea mays. EMBO J. 5, 835-841.
68. Perelson, A.S. & Bell, G.I. (1977) Mathematical models for the evolution of multigene families by unequal crossing over. Nature 265, 304-310.
69. Perticone, P., Gensabella, G. & Cozzi, R. (1997) Damage proneness induced by genomic DNA demethylation in mammalian cells cultivated in vitro. Mutagenesis 12, 259-264.
70. Petes, T.D., Detloff, P., Jinks-Robertson, S., et al (1989) Recombination in yeast and the recombinant DNA technology. Genome 31, 536-540.
71. Pirrotta, V. (1997) Chromatin-silencing mechanisms in Drosophila maintain patterns of gene expression. Trends Genet. 13, 314-318.
72. Preston, C.R. & Engels, W.R. (1989) Spread of P transposable elements in inbred lines of Drosophila melanogaster. Prog. Nucl. Acid Res. Mol. Biol. 36, 71-85.
73. Raina, R., Cook, D. & Fedoroff, N. (1993) Maize Spin transposable element has an enhancer-insensitive promoter. Proc. Natl. Acad. Sci. USA 90, 6355-6359.
74. Raina, R., Schläppi, M., Karunanandaa, B., Elhofy, A. & Fedoroff, N. (1998) Concerted formation of macromolecular Suppressor-mutator transposition complexes. Proc. Natl. Acad. Sci. USA 95, 8526-8531.
75. Richards, E.J. (1997) DNA methylation and plant development. Trends Genet. 13, 319-323.
76. Romero, D & Palacios, R. (1997) Gene amplification and genome plasticity in prokaryotes. Annu. Rev. Genet. 31, 91-111.
77. Ronchi, A., Petroni, K. & Tonelli, C. (1995) The reduced expression of endogenous duplications (REED) in the maize R gene family is mediated by DNA methylation. EMBO J. 14, 5318-5328.
78. Sabl, J.F. & Henikoff, S. (1996) Copy number and orientation determine the susceptibility of a gene to silencing by nearby heterochromatin in Drosophila. Genetics 142, 447-458.
79. SanMiguel, P., Tikhonov, A., Jin, Y.K., et al. (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765-768.
80. Saxena, R., Brown, E.G., Hawkins, T., et al. (1996) The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned. Nature Genet. 14, 292-299.
81. Schiebel, K., Winkelmann, M., Mertz, A., et al. (1997) Abnormal XY interchange between a novel isolated protein kinase gene, PRKY, and its homologue, PRKX, accounts for one third of all (Y+) XX males and (Y-) XY females. Hum. Mol. Genet. 6, 1985-1989.
82. Schläppi, M., Raina, R. & Fedoroff, N. (1994) Epigenetic regulation of the maize Spm transposable element: novel activation of a methylated promoter by TnpA. Cell 77, 427-437.
83. Schläppi, M., Raina, R. & Fedoroff, N. (1996) A highly sensitive plant hybrid protein assay system based on the Spm promoter and TnpA protein for detection and analysis of transcription activation domains. Plant Mol. Biol. 32, 717-725.
84. Schläppi, M., Smith, D. & Fedoroff, N. (1993) TnpA transactivates methylated maize Suppressor-mutator transposable elements in transgenic tobacco. Genetics 133, 1009-1021.
85. Schwartz, A., Chan, D.C., Brown, L.G., et al. (1998) Reconstructing hominid Y evolution: X-homologous block, created by X-Y transposition, was disrupted by Yp inversion through LINE-LINE recombination. Hum. Mol. Genet. 7, 1-11.
86. Selker, E.U. (1997) Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion? Trends Genet. 13, 296-301.
87. Shalev, G. & Levy, A.A. (1997) The maize transposable element Ac induces recombination between the donor site and an homologous ectopic sequence. Genetics 146, 1143-1151.
88. Sherman, J.M. & Pillus, L. (1997) An uncertain silence. Trends Genet. 13, 308-313.
89. Smit, A.F. (1996) The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6, 743-748.
90. Smit, A.F. & Riggs, A.D. (1996) Tiggers and DNA transposon fossils in the human genome. Proc. Natl Acad. Sci. USA 93, 1443-1448.
91. Smit, A.F., Toth, G., Riggs, A.D. & Jurka, J. (1995) Ancestral, mammalian- wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246, 401-417.
92. Tartof, K.D., Bishop, C., Jones, M., Hobbs, C.A. & Locke, J. (1989) Towards an understanding of position effect variegation. Dev. Genet. 10, 162-176.
93. Thuriaux, P. (1977) Is recombination confined to structural genes in the eukaryotic genome? Nature 268, 460-462.
94. Urieli-Shoval, S., Gruenbaum, Y., Sedat, J. & Razin, A. (1982) The absence of detectable methylated bases in Drosophila melanogaster DNA. FEES Lett. 146, 148-152.
95. Walker, E.L., Robbins, T.P., Bureau, T.E., Kermicle, J. & Dellaporta, S.L. (1995) Transposon-mediated chromosomal rearrangements and gene duplications in the formation of the maize R-r complex. EMBO J. 14, 2350-2363.
96. Wallrath, L.L. & Elgin, S.C. (1995) Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev. 9, 1263-1277.
97. Wolffe, A., ed. (1998) Epigenetics. New York: John Wiley & Sons.
98. Ye, F. & Signer, E.R. (1996) RIGS (repeat-induced gene silencing) in Arabidopsis is transcriptional and alters chromatin configuration. Proc. Natl. Acad. Sci. USA 93, 10881-10886.
99. Yoder, J.A., Walsh, C.P. & Bestor, T.H. (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13, 335-340.