The effect of stress on genome regulation and structure

Annals of Botany

Volumn 94, Issue 4, 2004, Pages 481-495

  Madlung, Andreas ^a,b   Comai, Luca ^b  

^a UNIVERSITY OF PUGET SOUND   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Allopolyploid; Genome; Genomic shock; Heterochromatin; Hybridization; Pathogen; Stress; Transposon

Indexed keywords

PHLOEM;

PLANT DNA; PLANT RNA;

CLIMATE; GENE SILENCING; GENETIC TRANSCRIPTION; GENETICS; GENOME; METABOLISM; MOLECULAR EVOLUTION; PLANT; PLANT DISEASE; POLYPLOIDY; REVIEW;

CLIMATE; DNA, PLANT; EVOLUTION, MOLECULAR; GENE SILENCING; GENOME, PLANT; PLANT DISEASES; PLANTS; POLYPLOIDY; RNA, PLANT; TRANSCRIPTION, GENETIC;

EID: 14744272333     PISSN: 03057364     EISSN: None     Source Type: Journal    
DOI: 10.1093/aob/mch172     Document Type: Review

References (136)

1. Aagaard L, Laible G, Selenko P, Schmid M, Dorn R, Schotta G, Kuhfittig S, Wolf A, Lebersorger A, Singh PB, et al. 1999. Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO Journal 18: 1923-1938.
2. Adams KL, Cronn R, Percifield R, Wendel JF. 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Science of the USA 100: 4649-4654.
3. Agrawal RK, Linde J, Sengupta J, Nierhaus KH, Frank J. 2001. Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation. Journal of Molecular Biology 311: 777-787.
4. Almeida J, Carpenter R, Robbins TP, Martin C, Coen ES. 1989. Genetic interactions underlying flower color patterns in Antirrhinum majus. Genes and Development 3: 1758-1767.
5. Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120-124.
6. Barbash DA, Siino DF, Tarone AM, Roote J. 2003. A rapidly evolving MYB-related protein causes species isolation in Drosophila. Proceedings of the National Academy of Science of the USA 100: 5302-5307.
7. Bartee L, Malagnac F, Bender J. 2001. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes and Development 15: 1753-1758.
8. Baulcombe D. 2002. Viral suppression of systemic silencing. Trends in Microbiology 10: 306-308.
9. Beguiristain T, Grandbastien MA, Puigdomenech P, Casacuberta JM. 2001. Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants. Plant Physiology 127: 212-221.
10. Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M. 1999. A mammalian protein with specific demethylase activity for mCpG DNA. Nature 397: 579-583.
11. Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes and Development 16: 6-21.
12. Bucheton A. 1995. The relationship between the flamenco gene and gypsy in Drosophila: how to tame a retrovirus. Trends in Genetics 11: 349-353.
13. Bushell C, Spielman M, Scott RJ. 2003. The basis of natural and artificial postzygotic hybridization barriers in Arabidopsis species. Plant Cell 15: 1430-1442.
14. Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. 2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology 13: 2212-2217.
15. Cao X, Jacobsen SE. 2002. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Current Biology 12: 1138-1144.
16. Cao X, Springer NM, Muszynski MG, Phillips RL, Kaeppler S, Jacobsen SE. 2000. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proceedings of the National Academy of Science of the USA 97: 4979-4984.
17. Chandler V, Rivin C, Walbot V. 1986. Stable non-mutator stocks of maize have sequences homologous to the Mu1 transposable element. Genetics 114: 1007-1021.
18. Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, Jacobsen SE, Fischer RL. 2002. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell 110: 33-42.
19. Coen ES, Carpenter R, Martin C. 1986. Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus. Cell 47: 285-296.
20. Comai L. 2000. Genetic and epigenetic interactions in allopolyploid plants. Plant Molecular Biology 43: 387-399.
21. Comai L, Madlung A, Josefsson C, Tyagi A. 2003. Do the different parental 'heteromes' cause genomic shock in newly formed allopolyploids? Philosophical Transactions of the Royal Society of London. Series B. Biological Science 358: 1149-1155.
22. Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, Byers B. 2000. Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell 12: 1551-1568.
23. Cullis CA. 1973. DNA differences between flax genotrophs. Nature 243: 515-516.
24. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC. 2000. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101: 543-553.
25. Dangl JL, Jones JD. 2001. Plant pathogens and integrated defence responses to infection. Nature 411: 826-833.
26. Dellaporta SL, Chomet PS, Mottinger JP, Wood JA, Yu SM, Hicks JB. 1984. Endogenous transposable elements associated with virus infection in maize. Cold Spring Harbor Symposium on Quantitative Biology 49: 321-328.
27. Escobar MA, Dandekar AM. 2003. Agrobacterium tumefaciens as an agent of disease. Trends in Plant Science 8: 380-386.
28. Fedoroff N, Schlappi M, Raina R. 1995. Epigenetic regulation of the maize Spm transposon. Bioessays 17: 291-297.
29. Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM. 1997. Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147: 1381-1387.
30. Finnegan EJ, Dennis ES. 1993. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Research 21: 2383-2388.
31. Finnegan EJ, Peacock WJ, Dennis ES. 1996. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proceedings of the National Academy of Science of the USA 93: 8449-8454.
32. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
33. Forsbach A, Schubert D, Lechtenberg B, Gils M, Schmidt R. 2003. A comprehensive characterization of single-copy T-DNA insertions in the Arabidopsis thaliana genome. Plant Molecular Biology 52: 161-176.
34. Galun E. 2003. Transposable elements. A guide for the perplexed and the novice. Boston, MA; Kluwer.
35. Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA. 2002. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297: 1871-1873.
36. Grandbastien MA. 1998. Activation of plant retrotransposons under stress conditions. Trends in Plant Science 3: 181-187.
37. Grandbastien MA, Lucas H, Morel JB, Mhiri C, Vernhettes S, Casacuberta JM. 1997. The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica 100: 241-252.
38. Greenberg JT, Vinatzer BA. 2003. Identifying type III effectors of plant pathogens and analyzing their interaction with plant cells. Current Opinions in Microbiology 6: 20-28.
39. Grewal SI, Moazed D. 2003. Heterochromatin and epigenetic control of gene expression. Science 301: 798-802.
40. Hammerle B, Ferrus A. 2003. Expression of enhancers is altered in Drosophila melanogaster hybrids. Evolution and Development 5: 221-230.
41. Harper G, Hull R, Lockhart B, Olszewski N. 2002. Viral sequences integrated into plant genomes. Annual Review in Phytopathology 40: 119-136.
42. Hashida SN, Kitamura K, Mikami T, Kishima Y. 2003. Temperature shift coordinately changes the activity and the methylation state of transposon Tam3 in Antirrhinum majus. Plant Physiology 132: 1207-1216.
43. He P, Friebe BR, Gill BS, Zhou JM. 2003. Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Molecular Biology 52: 401-414.
44. Hirochika H. 1993. Activation of tobacco retrotransposons during tissue culture. EMBO Journal 12: 2521-2528.
45. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M. 1996. Retrotransposons of rice involved in mutations induced by tissue culture. Proceedings of the National Academy of Science of the USA 93: 7783-7788.
46. Ivashuta S, Naumkina M, Gau M, Uchiyama K, Isobe S, Mizukami Y, Shimamoto Y. 2002. Genotype-dependent transcriptional activation of novel repetitive elements during cold acclimation of alfalfa (Medicago sativa). Plant Journal 31: 615-627.
47. Jackson JP, Lindroth AM, Cao X, Jacobsen SE. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
48. Jenuwein T, Allis CD. 2001. Translating the histone code. Science 293: 1074-1080.
49. Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR, Wessler SR. 2003. An active DNA transposon family in rice. Nature 421: 163-167.
50. Johns MA, Mottinger J, Freeling M. 1985. A low copy number, copia-like transposon in maize. EMBO Journal 4: 1093-1102.
51. Johnson L, Cao X, Jacobsen S. 2002. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Current Biology 12: 1360-1367.
52. Kaeppler SM, Phillips RL. 1993. Tissue culture-induced DNA methylation variation in maize. Proceedings of the National Academy of Science of the USA 90: 8773-8776.
53. Kaeppler SM, Kaeppler HF, Rhee Y. 2000. Epigenetic aspects of somaclonal variation in plants. Plant Molecular Biology 43: 179-188.
54. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH. 2000. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proceedings of the National Academy of Science of the USA 97: 6603-6607.
55. Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ. 2003. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163: 1109-1122.
56. Kashkush K, Feldman M, Levy AA. 2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659.
57. Kashkush K, Feldman M, Levy AA. 2003. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genetics 33: 102-106.
58. Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T. 2003. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Current Biology 13: 421-426.
59. Kidner CA, Martienssen RA. 2003. Macro effects of microRNAs in plants. Trends in Genetics 19: 13-16.
60. Kikuchi K, Terauchi K, Wada M, Hirano H. 2003. The plant MITE mPing is mobilized in anther culture. Nature 421: 167-170.
61. Kimura RH, Choudary PV, Schmid CW. 1999. Silk worm Bm1 SINE RNA increases following cellular insults. Nucleic Acids Research 27: 3380-3387.
62. Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Fischer RL, Kakutani T. 2004. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303: 521-523.
63. Kitamura K, Hashida SN, Mikami T, Kishima Y. 2001. Position effect of the excision frequency of the Antirrhinum transposon Tam3: implications for the degree of position-dependent methylation in the ends of the element. Plant Molecular Biology 47: 475-490.
64. Kovalchuk I, Kovalchuk O, Kalck V, Boyko V, Filkowski J, Heinlein M, Hohn B. 2003. Pathogen-induced systemic plant signal triggers DNA rearrangements. Nature 423: 760-762.
65. Kubis SE, Castilho AM, Vershinin AV, Heslop-Harrison JS. 2003. Retro-elements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Molecular Biology 52: 69-79.
66. Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T. 2001. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116-120.
67. Laufs P, Autran D, Traas J. 1999. A chromosomal paracentric inversion associated with T-DNA integration in Arabidopsis. Plant Journal 18: 131-139.
68. Lee HS, Chen ZJ. 2001. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proceedings of the National Academy of Science of the USA 98: 6753-6758.
69. Lee M, Phillips RL. 1988. The chromosomal basis of somaclonal variation. Annual Review in Plant Physiology and Plant Molecular Biology 39: 413-437.
70. Lindbo JA, Fitzmaurice WP, della-Cioppa G. 2001. Virus-mediated reprogramming of gene expression in plants. Current Opinion in Plant Biology 4: 181-185.
71. Lindbo JA, Silva-Rosales L, Proebsting WM, Dougherty WG. 1993. Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. Plant Cell 5: 1749-1759.
72. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080.
73. Lippman Z, May B, Yordan C, Singer T, Martienssen R. 2003. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biology 1: E67.
74. Liu B, Wendel JF. 2000. Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome 43: 874-880.
75. Liu B, Wendel JF. 2003. Epi genetic phenomena and the evolution of plant allopolyploids. Molecular Phylogenetics and Evolution 29: 365-379.
76. Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF. 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44: 321-330.
77. Liu B, Vega JM, Feldman M. 1998. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome 41: 535-542.
78. Lucht JM, Mauch-Mani B, Steiner HY, Metraux JP, Ryals J, Hohn B. 2002. Pathogen stress increases somatic recombination frequency in Arabidopsis. Nature Genetics 30: 311-314.
79. McClintock B. 1968. The states of a gene locus in maize. Carnegie Institute of Washington Yearbook 66: 20-28.
80. McClintock B. 1984. The significance of responses of the genome to challenge. Science 226: 792-801.
81. Madlung A, Masuelli RW, Watson B, Reynolds SH, Davison J, Comai L. 2002. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiology 129: 733-746.
82. Manzur KL, Farooq A, Zeng L, Plotnikova O, Koch AW, Sachchidanand, Zhou MM. 2003. A dimeric viral SET domain raethyltransferase specific to Lys27 of histone H3. Nature Structural Biology 10: 187-196.
83. Martienssen RA. 2003. Maintenance of heterochromatin by RNA interference of tandem repeats. Nature Genetics 35: 213-214.
84. Martienssen R, Barkan A, Taylor WC, Freeling M. 1990. Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize. Genes and Development 4: 331-343.
85. Masson P, Surosky R, Kingsbury JA, Fedoroff NV. 1987. Genetic and molecular analysis of the Spm-dependent a-m2 alleles of the maize a locus. Genetics 117: 117-137.
86. Mayer W, Niveleau A, Walter J, Fundele R, Haaf T. 2000. Demethylation of the zygotic paternal genome. Nature 403: 501-502.
87. Meins F. 1983. Heritable variation in plant cell culture. Annual Review in Plant Physiology 34: 327-346.
88. Melayah D, Bonnivard E, Chalhoub B, Audeon C, Grandbastien MA. 2001. The mobility of the tobacco Tnt1 retrotransposon correlates with its transcriptional activation by fungal factors. Plant Journal 28: 159-168.
89. Michaud EJ, van Vugt MJ, Bultman SJ, Sweet HO, Davisson MT, Woychik RP. 1994. Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. Genes and Development 8: 1463-1472.
90. Miura A, Kato M, Watanabe K, Kawabe A, Kotani H, Kakutani T. 2004. Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana. Molecular Genetics and Genomes 270: 524-532.
91. Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T. 2001. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212-214.
92. Mottinger JP, Johns MA, Freeling M. 1984. Mutations of the Adh1 gene in maize following infection with barley stripe mosaic virus. Molecular and General Genetics 195: 367-369.
93. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, et al. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533-542.
94. Nacry P, Camilleri C, Courtial B, Caboche M, Bouchez D. 1998. Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics 149: 641-650.
95. Napoli C, Lemieux C, Jorgensen R. 1990. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2: 279-289.
96. Oh TJ, Cullis CA. 2003. Labile DNA sequences in flax identified by combined sample representational difference analysis (csRDA). Plant Molecular Biology 52: 527-536.
97. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee HS, Comai L, Madlung A, Doerge RW, et al. 2003. Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 19: 141-147.
98. Oswald J, Engemann S, Lane N, Mayer W, Olek A, Fundele R, Dean W, Reik W, Walter J. 2000. Active demethylation of the paternal genome in the mouse zygote. Current Biology 10: 475-478.
99. Ozkan H, Levy AA, Feldman M. 2001. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13: 1735-1747.
100. Pal-Bhadra M, Leibovitch BA, Gandhi SG, Rao M, Bhadra U, Birchler JA, Elgin SC. 2004. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303: 669-672.
101. Pauls PK, Kunert K, Huttner E, Grandbastien MA. 1994. Expression of the tobacco Tnt1 retrotransposon promoter in heterologous species. Plant Molecular Biology 26: 393-402.
102. Ramchandani S, Bhattacharya SK, Cervoni N, Szyf M. 1999. DNA methylation is a reversible biological signal. Proceedings of the National Academy of Science of the USA 96: 6107-6112.
103. Richert-Poggeler KR, Shepherd RJ. 1997. Petunia vein-clearing virus: a plant pararetrovirus with the core sequences for an integrase function. Virology 236: 137-146.
104. Riddle NC, Birchler JA. 2003. Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids. Trends in Genetics 19: 597-600.
105. Schauer SE, Jacobsen SE, Meinke DW, Ray A. 2002. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends in Plant Science 7: 487-491.
106. Schramke V, Allshire R. 2003. Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301: 1069-1074.
107. Schranz ME, Osborn TC. 2000. Novel flowering time variation in the resynthesized polyploid Brassica napus. Journal of Heredity 91: 242-246.
108. Scowcroft WRB, Brettell RIS, Ryan SA, Davies PAP, Pallotta MA. 1986. Somaclonal variation and genomic flux. Plant Biology, New York 3: 275-286.
109. Seitz H, Youngson N, Lin SP, Dalbert S, Paulsen M, Bachellerie JP, Ferguson-Smith AC, Cavaille J. 2003. Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nature Genetics 34: 261-262.
110. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA. 2001. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749-1759.
111. Shen WH. 2001. NtSET1, a member of a newly identified subgroup of plant SET-domain-containing proteins, is chromatin-associated and its ectopic overexpression inhibits tobacco plant growth. Plant Journal 28: 371-383.
112. Singer T, Yordan C, Martienssen RA. 2001. Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes and Development 15: 591-602.
113. Song K, Lu P, Tang K, Osborn TC. 1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proceedings of the National Academy of Science of the USA 92: 7719-7723.
114. Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ. 2000. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Molecular Cell 6: 791-802.
115. Suoniemi A, Narvanto A, Schulman AH. 1996. The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Molecular Biology 31: 295-306.
116. Szurek B, Marois E, Bonas U, Van den Ackerveken G. 2001. Eukaryotic features of the Xanthomonas type III effector AvrBs3: protein domains involved in transcriptional activation and the interaction with nuclear import receptors from pepper. Plant Journal 26: 523-534.
117. Takeda S, Sugimoto K, Otsuki H, Hirochika H. 1998. Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate. Plant Molecular Biology 36: 365-376.
118. Takeda S, Sugimoto K, Otsuki H, Hirochika H. 1999. A 13-bp cis-regulatory element in the LTR promoter of the tobacco retrotransposonTto1 is involved in responsiveness to tissue culture, wounding, methyl jasmonate and fungal elicitors. Plant Journal 18: 383-393.
119. Tax FE, Vernon DM. 2001. T-DNA-associated duplication/translocations in Arabidopsis. Implications for mutant analysis and functional genomics. Plant Physiology 126: 1527-1538.
120. Tijsterman M, Ketting RF, Plasterk RH. 2002. The genetics of RNA silencing. Annual Review in Genetics 36: 489-519.
121. Tompa R, McCallum CM, Delrow J, Henikoff JG, van Steensel B, Henikoff S. 2002. Genome-wide profiling of DNA methylationreveals transposon targets of CHROMOMETHYLASE3. Current Biology 12: 65-68.
122. Vaistij FE, Jones L, Baulcombe DC. 2002. Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell 14: 857-867.
123. Vargason JM, Szittya G, Burgyan J, Tanaka Hall TM. 2003. Size selective recognition of siRNA by an RNA silencing suppressor. Cell 115: 799-811.
124. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D. 2004. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303: 672-676.
125. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833-1837.
126. Vongs A, Kakutani T, Martienssen RA, Richards EJ. 1993. Arabidopsis thaliana DNA methylation mutants. Science 260: 1926-1928.
127. Voytas F, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae. In: Craig N, Craigie R, Gellert M, Lambowitz AM, eds. Mobile DNA II. Washington, DC: ASM Press, 631-662.
128. Wassenegger M, Heimes S, Riedel L, Sanger HL. 1994. RNA-directed de novo methylation of genomic sequences in plants. Cell 76: 567-576.
129. Whitelaw E, Martin DI. 2001. Retrotransposons as epigenetic mediators of phenotypic variation in mammals. Nature Genetics 27: 361-365.
130. Witte CP, Le QH, Bureau T, Kumar A. 2001. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proceedings of the National Academy of Science of the USA 98: 13778-13783.
131. Wojtaszek P. 1997. Oxidative burst: an early plant response to pathogen infection. Biochemistry Journal 322: 681-692.
132. Xiong LZ, Xu CG, Saghai Maroof MA, Zhang Q. 1999. Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Molecular and General Genetics 261: 439-446.
133. Yamashita S, Takano-Shimizu T, Kitamura K, Mikami T, Kishima Y. 1999. Resistance to gap repair of the transposon Tam3 in Antirrhinum majus: a role of the end regions. Genetics 153: 1899-1908.
134. Ye K, Malinina L, Patel DJ. 2003. Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature 426: 874-878.
135. Zemach A, Grafi G. 2003. Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant Journal 34: 565-572.
136. Zhu B, Zheng Y, Angliker H, Schwarz S, Thiry S, Siegmann M, Jost JP. 2000. 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Nucleic Acids Research 28: 4157-4165.