Epigenetics and its implications for plant biology. 1. The epigenetic network in plants

Annals of Botany

Volumn 96, Issue 7, 2005, Pages 1143-1164

  Grant Downton, R T ^a   Dickinson, H G ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Chromatin; DNA methylation; Epigenetics; Gene expression; Histones; Paramutation; RNA; Silencing; Transgenes

Indexed keywords

HISTONE; PLANT RNA;

GENE EXPRESSION;

ALLELE; CHIMERA; DNA METHYLATION; DNA PACKAGING; GENE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; HISTONE CODE; PHYSIOLOGY; PLANT; REVIEW; TRANSGENE;

ALLELES; CHIMERA; DNA METHYLATION; DNA PACKAGING; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENES, PLANT; HISTONE CODE; HISTONES; PLANTS; RNA, PLANT; TRANSGENES; VARIATION (GENETICS);

EID: 27944470090     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mci273     Document Type: Review

References (181)

1. Aalfs JD, Kingston RE. 2000. What does 'chromatin remodeling' mean? Trends in Biochemical Sciences 25: 548-555.
2. Adams S, Vinkenoog R, Spielman M, Dickinson HG, Scott RJ. 2000. Parent-of-origin effects on seed development in Arabidopsis require DNA methylation. Development 127: 2493-2502.
3. Alleman M, Doctor J. 2000. Genomic imprinting in plants: observations and evolutionary implications. Plant Molecular Biology 43: 147-161.
4. Amedeo P, Habu Y, Afsar K, Mittelsten Scheid O, Paszkowski J. 2000. Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405: 203-206.
5. Anandalakshmi R, Marathe R, Ge X, Herr Jr JM, Mau C, Mallory A, et al. 2000. A calmodulin-related protein that suppresses post-transcriptional gene silencing in plants. Science 290: 142-144.
6. Anderson LK, Stack SM. 2002. Meiotic recombination in plants. Current Genomics 3: 507-525.
7. Antequera F, Bird AP. 1988. Unmethylated CpG islands associated with genes in higher plant DNA. EMBO Journal 7: 2295-2299.
8. Ascenzi R, Gantt JS. 1999. Subnuclear distribution of the entire complement of linker histone variants in Arabidopsis thaliana. Chromosoma 108: 345-355.
9. Ashikawa I. 2001. Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. The Plant Journal 26: 617-625.
10. Bao N, Lye K-W, Barton M. 2004. MicroRNA binding sites in Arabidopsis class III HD-Zip mRNAs are required for methylation of the template chromosome. Developmental Cell 7: 653-662.
11. Bartee L, Bender J. 2001. Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family. Nucleic Acids Research 29: 2127-2134.
12. Baulcombe D. 2004. RNA silencing in plants. Nature 431: 356-363.
13. Bender J. 2004. Chromatin-based silencing mechanisms. Current Opinion in Plant Biology 7: 521-526.
14. Bennett MD. 1988. Parental genome separation in F1 hybrids between grass species. In: Brandham PE, ed. Proceedings of Kew Chromosome Conference III. London: HMSO, 195-208.
15. Berg A, Meza T, Mahic M, Thorstensen T, Kristiansen K, Aalen R. 2003. Ten members of the Arabidopsis gene family encoding methyl-CpG-binding domain proteins are transcriptionally active and at least one, AtMBD11, is crucial for normal development. Nucleic Acids Research 31: 5291-5304.
16. Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M. 1999. A mammalian protein with specific demethylase activity for mCpG DNA. Nature 397: 579-583.
17. Bollman K, Aukerman M, Park M, Hunter C, Berardini T, Poethig R. 2003. HASTY, the Arabidopsis ortholog of exportin-5/MSN5, regulates phase change and morphogenesis. Development 130: 1493-1504.
18. Boutet S, Vazquez F, Liu J, Béclin C, Fagard M, Gratias A, et al. 2003. Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Current Biology 13: 843-848.
19. Bowler C, Benvuento G, Lafalmme P, Molino D, Probst A, Tariq M, et al. 2004. Chromatin techniques for plant cells. The Plant Journal 39: 776-789.
20. Braunstein TH, Moury B, Johannessen M, Albrechtsen M. 2002. Specific degradation of 3′ regions of GUS mRNA in posttranscriptionally silenced tobacco lines may be related to 5′-3′ spreading of silencing. RNA 8: 1034-1044.
21. Burn JE, Bagnall DJ, Metzger JM, Dennis ES, Peacock WJ. 1993. DNA methylation, vernalization, and the initiation of flowering. Proceedings of the National Academy of Sciences of the USA 90: 287-291.
22. Bushell C, Spielman M, Scott R. 2003. The basis of natural and artificial postzygotic hybridization barriers in Arabidopsis species. The Plant Cell 15: 1430-1442.
23. Cao X, Jacobsen S. 2002a. Locus specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proceedings of the National Academy of Sciences of the USA 99: 16491-16498.
24. Cao X, Jacobsen SE. 2002b. Role of Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Current Biology 12: 1138-1144.
25. Carmell MA, Xuan Z, Zhang MQ, Hannon GJ. 2002. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance and tumorigenesis. Genes and Development 16: 2733-2742.
26. Cervoni N, Bhattacharya S, Szyf M. 1999. DNA demethylase is a processive enzyme. Journal of Biological Chemistry 274: 8363-8366.
27. Chandler V, Stain M. 2004. Chromatin conversations: mechanisms and implications of paramutation. Nature Reviews Genetics 5: 532-544.
28. Chandler VL, Eggleston WB, Dorweiler JE. 2000. Paramutation in maize. Plant Molecular Biology 43: 121-145.
29. Chen ZJ, Pikaard CS. 1997a. Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes and Development 11: 2124-2136.
30. Chen ZJ, Pikaard CS. 1997b. Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proceedings of the National Academy of Sciences of the USA 94: 3442-3447.
31. Chen ZJ, Comai L, Pikaard CS. 1998. Gene dosage and stochastic effects determine the severity and direction of uniparental rRNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proceedings of the National Academy of Sciences of the USA 95: 14891-14896.
32. Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, et al. 2002. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110: 33-42.
33. Chua Y, Mott E, Brown A, MacLean D, Gray J. 2004. Microarray analysis of chromatin-immunprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. The Plant Journal 37: 789-800.
34. Comai L, Tygai AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, et al. 2000. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. The Plant Cell 12: 1551-1567.
35. Cubas P, Vincent C, Coen E. 1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157-161.
36. Cui H, Fedoroff N. 2002. Inducible DNA demethylation mediated by the maize Suppressor-mutator transposon-encoded TnpA protein. The Plant Cell 14: 2883-2899.
37. 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.
38. Dalmay T, Horsefield R, Hartig Braunstein T, Baulcombe DC. 2001. SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. EMBO Journal 20: 2069-2077.
39. D'Amato F. 1991. Nuclear changes in cultured plant cells. Caryologica 44: 217-224.
40. Dilkes B, Comai L. 2004. A differential dosage hypothesis for parental effects in seed development. The Plant Cell 16: 3174-3180.
41. Dorweiler JE, Carey CC, Kubo KM, Hollick JB, Kermicle JL, Chandler VL. 2000. mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. The Plant Cell 12: 2101-2118.
42. Dugas D, Bartel B. 2004. MicroRNA regulation of gene expression in plants. Current Opinion in Plant Biology 7: 512-520.
43. Dunoyer P, Lecellier C-H, Parizotto E-A, Himber C, Voinnet O. 2004. Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. The Plant Cell 16: 1235-1250.
44. Fagard M, Vaucheret H. 2000. (Trans)gene silencing in plants: how many mechanisms? Annual Review of Plant Physiology and Plant Molecular Biology 51: 167-174.
45. Fagard M, Boutet S, Morel J-B, Bellini C, Vaucheret H. 2000. AGO1, QDE2 and RDE1 are related proteins required for post-transcriptonal gene silencing in plants, quelling in fungi, and RNA interference in animals. Proceedings of the National Academy of Sciences of the USA 97: 11650-11654.
46. Fan JY, Gordon F, Luger K, Hansen JC, Tremethick DJ. 2002. The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Nature Structural Biology 9: 172-176.
47. Finnegan EJ, Genger RK, Peacock WJ, Dennis ES. 1998. DNA methylation in plants. Annual Review of Plant Physiology and Plant Molecular Biology 49: 223-247.
48. Finnegan EJ, Peacock WJ, Dennis ES. 1996. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proceedings of the National Academy of Sciences of the USA 93: 8449-8454.
49. Fransz P, de Jong JH, Lysak M, Castiglione MR, Schubert I. 2002. Interphase chromosomes in Arabidopsis are organised as well-defined chromocenters from which euchromatin loops emanate. Proceedings of the National Academy of Sciences of the USA 99: 14584-14589.
50. Frommer M, McDonald L, Millar D, Collis C, Watt F, Grigg G, et al. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcyosine residues in individual strands. Proceedings of the National Academy of Sciences of the USA 89: 1827-1831.
51. Furner IJ, Sheikh MA, Collett CE. 1998. Gene silencing and homology-dependent gene silencing in Arabidopsis: genetic modifiers and DNA methylation. Genetics 149: 651-662.
52. García-Pérez RD, Van Houdt H, Depicker A. 2004. Spreading of post-transcriptional gene silencing along the target gene promotes systemic silencing. The Plant Journal 38: 594-602.
53. Gazzani S, Lawrenson T, Woodward C, Headon D, Sablowski R. 2004. A link between mRNA turnover and RNA interference in Arabidopsis. Science 306: 1046-1048.
54. Gehring M, Choi Y, Fischer R. 2004. Imprinting and seed development. The Plant Cell 16: S203-S213.
55. Genger RK, Kovac KA, Dennis ES, Peacock WJ, Finnegan EJ. 1999. Multiple DNA methyltransferases in Arabidopsis thaliana. Plant Molecular Biology 41: 269-278.
56. Gong Z, Morales-Ruiz T, Ariza R, Roldán-Arjona T, David L, Zhu J-K. 2002. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111: 803-814.
57. Goodrich J, Tweedie S. 2002. Remembrance of things past: chromatin remodelling in plant development. Annual Review of Cell and Developmental Biology 18: 707-746.
58. Gosselé V, Faché I, Meulewaeter F, Cornelissen M, Metzlaff M. 2002. SVISS - a novel transient gene silencing system for gene function discovery and validation in tobacco plants. The Plant Journal 32: 859-866.
59. Grant V. 1981. Plant speciation. New York, Columbia University Press.
60. Grant-Downton R, Dickinson H. 2004. Plants, pairing and phenotypes: two's company? Trends in Genetics 20: 188-195.
61. Grossniklaus U, Spillane C, Page DR, Kohler C. 2001. Genomic imprinting and seed development: endosperm formation with and without sex. Current Opinion in Plant Biology 4: 21-27.
62. Gruenbaum Y, Naveh-Many T, Cedar H, Razin A. 1981. Sequence specificity of methylation in higher plant DNA. Nature 292: 860-862.
63. Gutierrez-Marcos J, Pennington P, Costa L, Dickinson H. 2003. Imprinting in the endosperm: a possible role in preventing wide hybridization. Philosophical Transactions of the Royal Society of London, Series B 358: 1105-1112.
64. Haig D, Westoby M. 1989. Parent-specific gene expression and the triploid endosperm. The American Naturalist 134: 147-155.
65. Haig D, Westoby M. 1991. Genomic imprinting in endosperm: its effect on seed development in crosses between species, and between different ploidies of the same species, and its implications for the evolution of apomixis. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 333: 1-13.
66. Hamilton AJ, Baulcombe DC. 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286: 950-952.
67. Hamilton A, Voinnet O, Chappell L, Baulcombe D. 2002. Two classes of short interfering RNA in RNA silencing. EMBO Journal 21: 4671-4679.
68. Han M-H, Goud S, Song L, Fedoroff N. 2004. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proceedings of the National Academy of Sciences of the USA 101: 1093-1098.
69. Hasterok R, Maluszynska J. 2000. Nucleolar dominance does not occur in root tip cells of Brassica allotetraploids. Genome 43: 574-579.
70. Haupt W, Fischer TC, Winderl S, Fransz P, Torres-Ruiz RA. 2001. The CENTROMERE1 (CEN1) region of Arabidopsis thaliana: architecture and functional impact of chromatin. The Plant Journal 27: 285-296.
71. Henikoff S, Furuyama T, Ahmad K. 2004. Histone variants, nucleosome assembly and epigenetic inheritance. Trends in Genetics 20: 320-326.
72. Herr A, Jensen M, Dalmay T, Baulcombe D. 2005. RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120.
73. Heslop-Harrison JS. 1990. Gene expression and parental dominance in hybrid plants. Development Suppl.: Genomic Imprinting 21-28.
74. Hollick JB, Chandler VL. 2001. Genetic factors required to maintain repression of a paramutagenic maize pl allele. Genetics 157: 369-378.
75. Hollick JB, Dorweiler JE, Chandler VL. 1997. Paramutation and related allelic interactions. Trends in Genetics 13: 302-308.
76. Horn PJ, Peterson CL. 2002. Chromatin higher-order folding: wrapping up transcription. Science 297: 1824-1827.
77. Hsieh T-F, Hakim O, Fischer R. 2003. From flour to flower: how Polycomb group proteins influence multiple aspects of plant development. Trends in Plant Science 8: 439-445.
78. Jablonka E, Lamb MJ. 2002. The changing concept of epigenetics. Annals of the New York Academy of Sciences 981: 82-96.
79. Jackson JP, Lindroth AM, Cao X, Jacobsen SE. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
80. Jacobsen SE, Meyerowitz EM. 1997. Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277: 1100-1103.
81. Jacobsen SE, Sakai H, Finnegan EJ, Cao X, Meyerowitz EM. 2000. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Current Biology 10: 179-186.
82. Jeddeloh JA, Stokes TL, Richards EJ. 1999. Maintenance of genomic methylation requires a SW12/SN2-like protein. Nature Genetics 22: 94-97.
83. Jenuwein T, Allis D. 2001. Translating the histone code. Science 293: 1074-1080.
84. Jones L, Hamilton AJ, Voinnet O, Thomas CL, Maule AJ, Baulcombe DC. 1999. RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing. The Plant Cell 11: 2291-2302.
85. Jones L, Ratcliff F, Baulcombe DC. 2001. RNA-directed transcriptional silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Current Biology 11: 747-757.
86. Jorgensen R, Cluster P, English J, Que Q, Napoli C. 1996. Chalcone synthase co-suppression phenotypes in Petunia flowers: comparison of sense vs. antisense constructs and single copy vs. complex T-DNA sequences. Plant Molecular Biology 31: 957-973.
87. Kaeppler SM, Kaeppler HF, Rhee Y. 2000. Epigenetic aspects of somaclonal variation in plants. Plant Molecular Biology 43: 179-188.
88. Kakutani T, Jeddeloh J, Richards EJ. 1995. Characterisation of an Arabidopsis thaliana DNA hypomethylation mutant. Nucleic Acids Research 23: 130-137.
89. Kamakaka R. 2003. Heterochromatin: proteins in flux lead to stable repression. Current Biology 13: R317-R319.
90. Kamakaka R, Biggins S. 2005. Histone variants: deviants? Genes and Development 19: 295-310.
91. Kanno T, Mette M, Kreil D, Aufsatz W, Matzke M, Matzke A. 2004. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Current Biology 14: 801-805.
92. Katan-Khaykovich Y, Struhl K. 2005. Heterochromatin formation involves changes in histone modifications over multiple cell generations. EMBO Journal 24: 2138-2149.
93. Kidner C, Martienssen R. 2005. The developmental role of microRNAs in plants. Current Opinion in Plant Biology 8: 38-44.
94. Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen S, et al. 2004. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303: 521-523.
95. Kishimoto N, Sakai H, Jackson J, Jacobsen SE, Meyerowitz EM, Dennis ES, et al. 2001. Site specificity of the Arabidopsis MET1 DNA methyltransferase demonstrated through hypermethylation of the superman locus. Plant Molecular Biology 46: 171-183.
96. Klahre U, Crété P, Leuenberger SA, Iglesias VA, Meins Jr F. 2002. High molecular weight RNAs and small interfering RNAs induce systemic post-transcriptional gene silencing in plants. Proceedings of the National Academy of Sciences of the USA 99: 11981-11986.
97. Köhler C, Hennig L, Bouveret R, Gheyselinck J, Grossniklaus U, Gruissem W. 2003. Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development. EMBO Journal 22: 4804-4814.
98. Korber P, Hörz W. 2004. SWRed not shaken: mixing the histones. Cell 117: 5-7.
99. van der Krol A, Lenting P, Veenstra J, van der Meer I, Gerats A, Mol J, et al. 1988. An anti-sense chalcone synthase gene in transgenic plants inhibits flower pigmentation. Nature 333: 866-869.
100. van der Krol A, Mur L, Beld M, Mol J, Stuitje A. 1990. Flavonoid genes in Petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. The Plant Cell 2: 291-299.
101. Lawrence R, Earley K, Pontes O, Silva M, Chen Z, Neves N, et al. 2004. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Molecular Cell 13: 599-609.
102. Li G, Hall T, Holmes-Davis R. 2002. Plant chromatin: development and genme control. BioEssays 24: 234-243.
103. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, et al. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080.
104. Lindroth A, Shultis D, Jasencakova Z, Fuchs, J, Johnson L, Schubert D, et al. 2004. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO Journal 23: 4286-4296.
105. Lippman Z, Gendrel A-V, Black M, Vaughn M, Dedhla N, McComble R, et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
106. Lisch D, Carey CC, Dorweiler JE, Chandler V. 2002. A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing. Proceedings of the National Academy of Sciences of the USA 99: 6130-6135.
107. Loidl P. 2004. A plant dialect of the histone language. Trends in Plant Science 9: 84-90.
108. Lusser A, Kölle D, Loidl P. 2001. Histone acetylation: lessons from theplant kingdom. Trends in Plant Science 6: 59-65.
109. Malagnac F, Bartee L, Bender J. 2002. An Arabidopsis SET domain protein require for maintenance but not establishment of DNA methylation. EMBO Journal 21: 6842-6852.
110. Matzke M, Birchler J. 2005. RNAi-mediated pathways in the nucleus. Nature Genetics 6: 24-35.
111. Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette M, et al. 2004. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochimica et Biophysica Acta 1677: 129-141.
112. Mittelsten Scheid O, Probst AV, Afsar K, Paszkowski J. 2002. Two regulatory levels of transcriptional gene silencing in Arabidopsis. Proceedings of the National Academy of Sciences of the USA 99: 13659-13662.
113. Morel J-B, Godon C, Mourrain P, Béclin C, Boutet S, Feuerbach F, et al. 2002. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. The Plant Cell 14: 629-639.
114. Mourrain P, Béclin C, Elmayan T, Feuerbach F, Godon C, Morel J-B, et al. 2000. Arabidopsis SGS2 and SGS3 genes are required for post-transcriptional gene silencing and natural virus resistance. Cell 101: 533-542.
115. Murata M. 2002. Telomeres and centromeres in plants. Current Genomics 3: 527-538.
116. Murfett J, Wang X-J, Hagen G, Guilfoyle T. 2001. Identification of Arabidopsis histone deaceylase HDA6 mutants that affect transgene expression. The Plant Cell 13: 1047-1061.
117. Muskens MWM, Vissers APA, Mol JNM, Kooter JM. 2000. Role of inverted DNA repeats in transcriptional and post-transcriptional gene silencing. Plant Molecular Biology 43: 243-260.
118. Mysore KS, Nam J, Gelvin SB. 2000. An Arabidopsis histone H2A mutant is deficient in Agrobacterium T-DNA integration. Proceedings of the National Academy of Sciences of the USA 97: 948-953.
119. Nagaki K, Cheng Z, Ouyang S, Talbert P, Kim M, Jones K, et al. 2004. Sequencing of a rice centromere uncovers active genes. Nature Genetics 36: 138-145.
120. Nagaki K, Talbert P, Zhong C, Dawe R, Henikoff S, Jiang J. 2003. Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163: 1221-1225.
121. Nam J, Mysore KS, Zheng C, Knue MK, Matthyse AG, Gelvin SB. 1999. Identification of T-DNA tagged Arabidopsis mutants that are resistant to transformation by Agrobacterium. Molecular and General Genetics 261: 429-438.
122. Nan X, Ng H-H, Johnson CA, Laherty CD, Tuner BM, Eiseman RN, et al. 1998. Transcription repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393: 386-389.
123. Napoli C, Lemieux C, Jorgensen R. 1990. Introduction of the chalcone synthase gene into Petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2: 279-289.
124. Naumann K, Fischer A, Hofmann I, Krauss V, Phalke S, Irmler K, et al. 2005. Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO Journal 24: 1418-1429.
125. van Nocker S. 2003. CAF1 and MSI1-related proteins: linking nucleosome assembly with epigenetics. Trends in Plant Science 8: 471-473.
126. Onodera Y, Haag J, Ream T, Nunes P, Pontes O, Pikaard C. 2005. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120: 613-622.
127. Owen-Hughes T. 2003. Pathways for remodelling chromatin. Biochemical Society Transactions 31: 893-905.
128. Parker J, Roe S, Barford D. 2004. Crystal structure of a PIWI protein suggests mechanismsfor siRNA recognition and slicer activity. EMBO Journal 23: 4727-4737.
129. Paszkowski J, Whitham SA. 2001. Gene silencing and DNA methylation processes. Current Opinion in Plant Biology 4: 123-129.
130. Peragine A, Yoshikawa M, Wu G, Albrecht H, Poethig R. 2004. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes and Development 18: 2368-2379.
131. Pikaard C. 1999. Nucleolar dominance and silencing of transcription. Trends in Plant Science 4: 478-483.
132. Pikaard CS. 2000. Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids. Plant Molecular Biology 43: 163-177.
133. Pontes O, Lawrence R, Neves N, Silva M, Lee J-H, Chen Z, et al. 2003. Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis. Proceedings of the National Academy of Sciences of the USA 100: 11418-11423.
134. Probst AV, Fransz PF, Paszkowski J, Mittelsten Scheid O. 2003. Two means of transcriptional reactivation within heterochromatin. Plant Journal 33: 743-749.
135. Probst A, Fagard M, Proux F, Mourrain P, Boutet S, Earley K, et al. 2004. Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. The Plant Cell 16: 1021-1034.
136. Prymakowska-Bosak M, Przewloka MR, Slusarczyk J, Kurás M, Lichota J, Kiliańczyk B, et al. 1999. Linker histones play a role in male meiosis and the development of pollen grains in tobacco. The Plant Cell 11: 2317-2329.
137. Queitsch C, Sangster TA, Lindquist S. 2002. Hsp90 as a capacitor of phenotypic variation. Nature 417: 618-624.
138. Reik W, Dean W, Walter J. 2001. Epigenetic reprogramming in mammalian development. Science 293: 1089-1093.
139. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. 2002. Prediction of plant microRNA targets. Cell 110: 513-520.
140. Riggs CD. 1994. Molecular cloning of cDNAs encoding variants of meiotin-1: a meiotic protein associated with strings of nucleosomes. Chromosoma 103: 251-261.
141. Rocha P, Sheikh M, Melchiorre R, Fagard M, Boutet S, Loach R, et al. 2005. The Arabidopsis HOMOLOGY-DEPENDENT GENE SILENCING1 gene codes for an S-adenosyl-L-homocysteine hydrolase required for DNA methylation-dependent gene silencing. The Plant Cell 17: 404-417.
142. Ruffini Castiglione M, Cremonini R, Frediani M. 2002. DNA methylation patterns on plant chromosomes. Caryologica 55: 275-282.
143. Sasaki Y, Yasuda H, Ohba Y, Harada H. 1990. Isolation and characterisation of a novel nuclear protein in pollen mother cells of lily. Plant Physiology 94: 1467-1471.
144. Scebba F, Bernacchia G, De Bastiani M, Evangelista M, Cantoni RM, Cella R, et al. 2003. Arabidopsis MBD proteins show different binding specificities and nuclear localization. Plant Molecular Biology 53: 715-731.
145. 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.
146. Schubert D, Lechtenberg B, Forsbach A, Gils M, Bahadur S, Schmidt R. 2004. Silencing in Arabidopsis T-DNA transformants: the predominant role of a gene-specific RNA sensing mechanism versus position effects. The Plant Cell 16: 2561-2572.
147. Scott RJ, Spielman M, Bailey J, Dickinson HG. 1998. Parent-of-origin effects on seed development in Arabidopsis thaliana. Development 125: 3329-3341.
148. Shi Y, Lan F, Matson C, Mulligan P, Whetstine J, Cole P, et al. 2004. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119: 941-953.
149. Sidorenko LV, Peterson T. 2001. Transgene-induced silencing identifies sequences invoved in the establishment of paramutation of the maize p1 gene. The Plant Cell 13: 319-335.
150. Sijen T, Vijn I, Rebocho A, van Blokland R, Roelofs D, Mol J, et al. 2001. Transcriptional and post-transcriptional gene silencing are mechanistically related. Current Biology 11: 436-440.
151. Soppe WJJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, et al. 2002. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO Journal 21: 6549-6559.
152. Spielman M, Vinkenoog R, Dickinson H, Scott R. 2001. The epigenetic basis of gender in flowering plants and mammals. Trends in Genetics 17: 705-711.
153. Spielman M, Vinkenoog R, Scott RJ. 2003. Genetic mechanisms of apomixes. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 358: 1095-1103.
154. Stam M, Belele C, Dorweiler JE, Chandler VL. 2002. Differential chromatin structure within a tandem array 100kb upstream of the maize b1 locus is associated with paramutation. Genes and Development 16: 1906-1918.
155. Steimer A, Amedeo P, Afsar K, Fransz P, Mittelsten Scheid O, Paszkowski J. 2000. Endogenous targets of transcriptional gene silencing in Arabidopsis. The Plant Cell 12: 1165-1178.
156. Suzuki T, Ide N, Tanaka I. 1997. Immunocytochemical visualisation of the centromeres during male and female meiosis in Lilium longiflorum. Chromosoma 106: 434-445.
157. Szittya G, Silhavy D, Molnár A, Havelda Z, Lovas Á, Lakatos L, et al. 2003. Low temperature inhibits RNA silencing-mediated defence by the control of siRNA generation. EMBO Journal 22: 633-640.
158. Talbert PB, Masuelli R, Tygai AP, Comai L, Henikoff S. 2002. Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. The Plant Cell 14: 1053-1066.
159. Tanaka I, Akahori Y, Gomi K, Suzuki T, Ueda K. 1999. A novel histone variant localized in the nucleoli of higher plant cells. Chromosoma 108: 190-199.
160. Tang G, Reinhart BJ, Bartel DP, Zamore PD. 2003. A biochemical framework for RNA silencing in plants. Genes and Development 17: 49-63.
161. 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: 1265-1268.
162. Trewick S, McLaughlin P, Allshire R. 2005. Methylation: lost in hydroxylation? EMBO Reports 6: 315-319.
163. Turner BM. 2000. Histone acetylation and an epigenetic code. BioEssays 22: 836-845.
164. 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. The Plant Cell 14: 857-867.
165. Van Houdt H, Bleys A, Depicker A. 2003. RNA target sequences promote spreading of RNA silencing. Plant Physiology 131: 245-253.
166. Vaucheret H, Fagard M. 2001. Transcriptional gene silencing in plants: targets, inducers and regulators. Trends in Genetics 17: 29-35.
167. Vaucheret H, Vazquez F, Crete P, Bartel DP. 2004. The action of ARGONAUTE1 and its regulation by the miRNA pathway are crucial for plant development. Genes and Development 18: 1187-1197.
168. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory A, et al. 2004. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Molecular Cell 16: 69-79.
169. Vinkenoog R, Spielman M, Adams S, Dickinson HG, Scott RJ. 2000. Demethylation promotes autonomous endosperm development and rescues post-fertilization lethality in fie mutants. The Plant Cell 12, 2271-2282.
170. Vongs A, Kakutani T, Martienssen RA, Richards EJ. 1993. Arabidopsis thaliana DNA methylation deficient mutants. Science 260: 1926-1928.
171. Wassenegger M. 2000. RNA-directed DNA methylation. Plant Molecular Biology 43: 203-220.
172. Williams L, Carles C, Osmont K, Fletcher J. 2005. A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3 and ARF4 genes. Proceedings of the National Academy of Sciences of the USA 102: 9703-9708.
173. Wolffe AP, Pruss D. 1996. Deviant nucleosomes: the functional specialization of chromatin. Trends in Genetics 12: 58-62.
174. Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada J, et al. 2003. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Developmental Cell 5: 891-901.
175. Xie Z, Johansen L, Gustafson A, Kasschau K, Lellis A, Zilberman D, et al. 2004. Genetic and functional diversification of small RNA pathways in plants. Public Library of Science Biology 2: 642-652.
176. Yoo B-C, Kragler F, Varkonyi-Gasic E, Haywood V, Archer-Evans S, Lee Y, et al. 2004. A systemic small RNA signalling system in plants. The Plant Cell 16: 1979-2000.
177. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett R, et al. 2005. Methylation as a crucial step in plant microRNA biogenesis. Science 307: 932-935.
178. Zemach A, Grafi G. 2003. Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. The Plant Journal 34: 565-572.
179. Zemach A, Li Y, Wayburn B, Ben-Meir H, Kiss V, Avivi Y, et al. 2005. DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. The Plant Cell 17: 1549-1558.
180. Zhang X, Li X, Marshall J, Zong C, Dawe R. 2005. Phoshoserines on maize CENTROMERIC HISTONE H3 and histone H3 demarcate the centromere and pericentromere during chromosome segregation. The Plant Cell 17: 572-583.
181. Zilberman D, Cao X, Johansen L, Xie Z, Carrington J, Jacobsen S. 2004. Role of Arabidopsis in RNA-directed DNA methylation triggered by inverted repeats. Current Biology 14: 1214-1220.