Matrix Attachment Regions and Transcriptional Gene Silencing

Regulation of Transcription in Plants

Volumn 29, Issue , 2007, Pages 136-161

  Thompson, William F ^a   Spiker, Steven ^a   Allen, George C ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

Matrix attachment regions (MARS); Position effects; RNA polymerase; Transcriptional gene silencing (TGS); Transgene expression

Indexed keywords

EID: 84896867204     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470988886.ch6     Document Type: Chapter

References (169)

1. J.A. Able, C. Rathhus, B.J. Carroll and I.D. Godwin (2004) Sorghum Tissue Culture and Transformation (eds N. Seetharama and I. Godwin), p. 168. Science Publishers, Enfield, NH.
2. R. Abranches, R.W. Shultz, W.F. Thompson and G.C. Allen (2005) Matrix attachment regions and regulated transcription increase and stabilize transgene expression. Plant Biotechnology Journal 3, 535-543.
3. G.C. Allen, G. Hall, S. Michalowski, et al. (1996) High-level transgene expression in plant cells: effects of a strong scaffold attachment region from tobacco. The Plant Cell 8, 899-913.
4. G.C. Allen, G.E. Hall, L.C. Childs, A.K. Weissinger, S. Spiker and W.F. Thompson (1993) Scaffold attachment regions increase reporter gene expression in stably transformed plant cells. The Plant Cell 5, 603-613.
5. G.C. Allen, S. Spiker and W.F. Thompson (2000) Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Molecular Biology 43, 361-376.
6. B.B. Amati and S.M. Gasser (1988) Chromosomal ARS and CEN elements bind specifically to yeast nuclear scaffold. Cell 54, 967-978.
7. P. Amedeo, Y. Habu, K. Afsar, O. Mittelsten Scheid and J. Paszkowski (2000) Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405, 203-206.
8. S. Annadana, L. Mlynárová, M. Udayakumar, J. de Jong and J.P. Nap (2002) The potato Lhca3.St.1 promoter confers high and stable transgene expression in chrysanthemum, in contrast to CaMVbased promoters. Molecular Breeding 8, 335-344.
9. R. Ascenzi, B. Ülker, J.J. Todd, et al. (2003) Analysis of trans-silencing interactions using transcriptional silencers of varying strength and targets with and without flanking nuclear matrix attachment regions. Transgenic Research 12, 305-318.
10. C. Beclin, S. Boutet, P.Waterhouse and H.Vaucheret (2002)Abranched pathway for transgene-induced RNA silencing in plants. Current Biology 12, 684-688.
11. J. Bender (2004) Chromatin-based silencing mechanisms. Current Opinion in Plant Biology 7, 521-526.
12. C. Benham, T. Kohwi-Shigematsu and J. Bode (1997) Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions. Journal of Molecular Biology 274, 181-196.
13. J. Bode, C. Benham, A. Knopp and C. Mielke (2000) Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements). Critical Reviews in Eukaryotic Gene Expression 10, 73-90.
14. J. Bode, S. Winkelmann, S. Gotze, S. Spiker, K. Tsutsui, C. Bi, A.K. Prashanth and C. Benham (2006) Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy. Journal of Molecular Biology 358, 597-613.
15. C. Bonifer, N. Yannoutsos, G. Kruger, F. Grosveld and A.E. Sippel (1994) Dissection of the locus control function located on the chicken lysozyme gene domain in transgenic mice. Nucleic Acids Research 22, 4202-4210.
16. T. Boulikas (1993) Nature of DNA sequences at the attachment regions of genes to the nuclear matrix. Journal of Cellular Biochemistry 52, 14-22.
17. T. Boulikas (1995) Chromatin domains and prediction of MAR sequences. International Reviews in Cytology 162A, 279-388.
18. V. Bourdon, Z. Ladbrooke, A.Wickham, D. Lonsdale andW. Harwood (2002) Homozygous transgenic wheat plants with increased luciferase activity do not maintain their high level of expression in the next generation. Plant Science 163, 297-305.
19. P. Bregitzer and D. Tonks (2003) Inheritance and expression of transgenes in barley. Crop Science 43, 4-12.
20. P. Breyne, M. Van Montague, A. Depicker and G. Gheysen (1992) Characterization of a plant scaffold attachment region in a DNA fragment that normalizes transgene expression in tobacco. The Plant Cell 4, 463-471.
21. C. Brouwer, W. Bruce, S. Maddock, Z. Avramova and B. Bowen (2002) Suppression of transgene silencing by matrix attachment regions in maize: a dual role for the maize 5′ ADH1 matrix attachment region. The Plant Cell 14, 2251-2264.
22. C. Brun, Q. Dang and R. Miassod (1990) Studies of an 800-kilobase DNA stretch of the Drosophila X chromosome: comapping of a subclass of scaffold-attached regions with sequences able to replicate autonomously in Saccharomyces cerevisiae. Molecular and Cellular Biology 10, 5455-5463.
23. K.M.J. Butaye, I.J.W.M. Goderis, P.F.J. Wouters, et al. (2004) Stable high-level transgene expression in Arabidopsis thaliana using gene silencing mutants and matrix attachment regions. The Plant Journal 39, 440-449.
24. H.P. Cam, T. Sugiyama, E.S. Chen, X. Chen, P.C. FitzGerald and S.I.S. Grewal (2005) Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nature Genetics 37, 809-819.
25. Z.Q. Cheng, J. Targolli and R. Wu (2001) Tobacco matrix attachment region sequence increased transgene expression levels in rice plants. Molecular Breeding 7, 317-327.
26. A.M. Chinn, S.R. Payne and L. Comai (1996) Variegation and silencing of the heat shock cognate 80 gene are relieved by a bipartite downstream regulatory element. The Plant Journal 9, 325-339.
27. S.J. Clough and A.F. Bent (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. The Plant Journal 16, 735-743.
28. P.D. Cluster, M. O'Dell, M. Metzlaff and R.B. Flavell (1996) Details of T-DNA structural organization from a transgenic petunia population exhibiting co-suppression. Plant Molecular Biology 32, 1197-1203.
29. P.N. Cockerill and W.T. Garrard (1986) Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44, 273-282.
30. A.J. Conner, L. Mlynárová, W.J. Stiekema and J.P. Nap (1998) Meiotic stability of transgene expression is unaffected by flanking matrix-associated regions. Molecular Breeding 4, 47-58.
31. A.K. Csink and S. Henikoff (1996) Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature 381, 529-531.
32. C.D. Day, E. Lee, J. Kobayashi, L.D. Holappa, H. Albert and D.W. Ow (2000) Transgene integration into the same chromosome location can produce alleles that express at a predictable level, or alleles that are differentially silenced. Genes and Development 14, 2869-2880.
33. M.F.C. De Bolle, K.M.J. Butaye, W.J.W. Coucke, et al. (2003) Analysis of the influence of promoter elements and a matrix attachment region on the inter-individual variation of transgene expression in populations of Arabidopsis thaliana. Plant Science 165, 169-179.
34. S. De Buck, M. Van Montagu and A. Depicker (2001) Transgene silencing of invertedly repeated transgenes is released upon deletion of one of the transgenes involved. Plant Molecular Biology 46, 433-445.
35. S. De Buck, P. Windels, M. De Loose and A. Depicker (2004) Single-copy T-DNAs integrated at different positions in the Arabidopsis genome display uniform and comparable beta-glucuronidase accumulation levels. Cellular and Molecular Life Sciences 61, 2632-2645.
36. A.F. Dernburg, K.W. Broman, J.C. Fung, et al. (1996) Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85, 745-759.
37. D.R. Dorer and S. Henikoff (1994) Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77, 993-1002.
38. K.E. Francis and S. Spiker (2005) Identification of Arabidopsis thaliana transformants without selection reveals a high occurrence of silenced T-DNA integrations. The Plant Journal 41, 464-477.
39. P. Fransz, W. Soppe and I. Schubert (2003) Heterochromatin in interphase nuclei of Arabidopsis thaliana. Chromosome Research 11, 227-240.
40. Y. Fukuda and S. Nishikawa (2003) Matrix attachment regions enhance transcription of a downstream transgene and the accessibility of its promoter region to micrococcal nuclease. Plant Molecular Biology 51, 665-675.
41. S.M. Gasser and U.K. Laemmli (1986a) Cohabitation of scaffold binding regions with upstream/ enhancer elements of three developmentally regulated genes of Drosophila melanogaster. Cell 46, 521-530.
42. S.M. Gasser and U.K. Laemmli (1986b) The organisation of chromatin loops: characterization of a scaffold attachment site. The EMBO Journal 5, 511-518.
43. S. Gazzani, T. Lawrenson, C.Woodward, D. Headon and R. Sablowski (2004) A link between mRNA turnover and RNA interference in Arabidopsis. Science 306, 1046-1048.
44. P. Gepts (2002) A comparison between crop domestication, classical plant breeding, and genetic engineering. Crop Science 42, 1780-1790.
45. F. Girard, B. Bello, U.K. Laemmli and W.J. Gehring (1998) In vivo analysis of scaffold-associated regions in Drosophila: a synthetic high-affinity SAR binding protein suppresses position effect variegation. The EMBO Journal 17, 2079-2085.
46. G.V. Glazko, I.B. Rogozin and M.V. Glazkov (2001) Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix. Biochimica et Biophysica Acta 1517, 351-364.
47. H.S. Guo, J.F. Fei, Q. Xie and N.H. Chua (2003) A chemical-regulated inducible RNAi system in plants. The Plant Journal 34, 383-392.
48. G.E. Hall, Jr., G.C. Allen, D.S. Loer, W.F. Thompson and S. Spiker (1991) Nuclear scaffolds and scaffold-attachment regions in higher plants. Proceedings of the National Academy of Sciences of the United States of America 88, 9320-9324.
49. C. Halweg, W.F. Thompson and S. Spiker (2005) The Rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: a flow cytometric study. The Plant Cell 17, 418-429.
50. K.H. Han, C.P.Maand S.H. Strauss (1997) Matrix attachment regions (MARs) enhance transformation frequency and transgene expression in poplar. Transgenic Research 6, 415-420.
51. R. Hancock (2000) A new look at the nuclear matrix. Chromosoma 109, 219-225.
52. R. Hancock (2004) Internal organisation of the nucleus: assembly of compartments by macromolecular crowding and the nuclear matrix model. Biology of the Cell 96, 595-601.
53. S. Henikoff (1998) Conspiracy of silence among repeated transgenes. Bioessays 20, 532-535.
54. A.J. Herr, M.B. Jensen, T. Dalmay and D.C. Baulcombe (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308, 118-120.
55. R. Holmes-Davis and L. Comai (2002) The matrix attachment regions (MARs) associated with the heat shock cognate 80 gene (HSC80) of tomato represent specific regulatory elements. Molecular Genetics and Genomics 266, 891-898.
56. J. Hsieh and A. Fire (2000) Recognition and silencing of repeated DNA. Annual Reviews in Genetics 34, 187-204.
57. M.C. Huber, F.X. Bosch, A.E. Sippel and C. Bonifer (1994) Chromosomal position effects in chicken lysozyme gene transgenic mice are correlated with suppression of DNase I hypersensitive site formation. Nucleic Acids Research 22, 4195-4201.
58. V.A. Iglesias, E.A. Moscone, I. Papp, et al. (1997) Molecular and cytogenetic analyses of stably and unstably expressed transgene loci in tobacco. The Plant Cell 9, 1251-1264.
59. L.M. Iyer, S.P. Kumpatla, M.B. Chandrasekharan and T.C. Hall (2000) Transgene silencing in monocots. Plant Molecular Biology 43, 323-346.
60. D. Jackson (2005) Understanding nuclear organization: when information becomes knowledge. Workshop on nuclear organization. EMBO Reports 6, 213-217.
61. D.A. Jackson (2003) The principles of nuclear structure. Chromosome Research 11, 387-401.
62. S.E. Jacobsen (1999) Gene silencing: maintaining methylation patterns. Current Biology 9, R617-R619.
63. R.A. Jorgensen (2003) Sense cosuppression in plants: past, present, and future. In: RNAi: A guide to gene silencing (ed. G.J. Hannon), pp. 5-22. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
64. A. Kerschen, C.A. Napoli, R.A. Jorgensen and A.E. Muller (2004) Effectiveness of RNA interference in transgenic plants. FEBS Letters 566, 223-228.
65. C.A. Kidner and R.A. Martienssen (2005) The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Developmental Biology 280, 504-517.
66. W.S. Kim, J. Kim, H.B. Krishnan and B.H. Nahm (2005) Expression of Escherichia coli branching enzyme in caryopses of transgenic rice results in amylopectin with an increased degree of branching. Planta 220, 689-695.
67. C. Lacomme, K. Hrubikova and I. Hein (2003) Enhancement of virus-induced gene silencing through viral-based production of inverted-repeats. The Plant Journal 34, 543-553.
68. V. Levee, E. Garin, K. Klimaszewska and A. Seguin (1999) Stable genetic transformation of white pine (Pinus strobus L.) after cocultivation of embryogenic tissues with Agrobacterium tumefaciens. Molecular Breeding 5, 429-440.
69. J.S. Levin, W.F. Thompson, A.S. Csinos, M.G. Stephenson and A.K. Weissinger (2005) Matrix attachment regions increase the efficiency and stability of RNA-mediated resistance to tomato spotted wilt virus in transgenic tobacco. Transgenic Research 14, 193-206.
70. I. Liebich, J. Bode, I. Reuter and E. Wingender (2002) Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs). Nucleic Acids Research 30, 3433-3442.
71. J.A. Lindbo, L. Silva-Rosales, W.M. Proebsting and W.G. Doughtery (1993) Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. The Plant Cell 5, 1749-1759.
72. Z. Lippman, B. May, C. Yordan, T. Singer and R. Martienssen (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biology 1, E67.
73. J.W. Liu and L.M. Tabe (1998) The influences of two plant nuclear matrix attachment regions (MARs) on gene expression in transgenic plants. Plant and Cell Physiology 39, 115-123.
74. A. Lorence and R. Verpoorte (2004) Gene transfer and expression in plants. Methods in Molecular Biology 267, 329-350.
75. L.M. Mankin, G.C. Allen and W.F. Thompson (1997) Introducton of a plant intron into the luciferase gene of Photinus pyralis. Plant Molecular Biology Reporter 15, 186-196.
76. S.L. Mankin, G.C. Allen, T. Phelan, S. Spiker and W.F. Thompson (2003) Elevation of transgene expression level by flanking matrix attachment regions (MAR) is promoter dependent: a study of the interactions of six promoters with the RB7 3′ MAR. Transgenic Research 12, 3-12.
77. A.M. Martelli, E. Falcieri, M. Zweyer, et al. (2002) The controversial nuclear matrix: a balanced point of view. Histology and Histopathology 17, 1193-1205.
78. R.A. Martienssen (2003) Maintenance of heterochromatin by RNA interference of tandem repeats. Nature Genetics 35, 213-214.
79. T. Masaki, H. Tsukagoshi, N. Mitsui, et al. (2005) Activation tagging of a gene for a protein with novel class of CCT-domain activates expression of a subset of sugar-inducible genes in Arabidopsis thaliana. The Plant Journal 43, 142-152.
80. M.A. Matzke, W. Aufsatz, T. Kanno, M.F. Mette and A.J. Matzke (2002) Homology-dependent gene silencing and host defense in plants. Advances in Genetics 46, 243-275.
81. M.A. Matzke and J.A. Birchler (2005) RNAi-mediated pathways in the nucleus. Nature Reviews Genetics 6, 24-35.
82. M.A. Matzke, M.F. Mette and A.J.M. Matzke (2000) Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates. Plant Molecular Biology 43, 401-415.
83. M.A. Matzke, M. Primig, J. Trnovsky and A.J.M. Matzke (1989) Reversible methylation and inactivation of marker genes in sequentially transformed tobacco plants. The EMBO Journal 8, 643-649.
84. S. Maximova, C. Miller, G. Antunez de Mayolo, S. Pishak, A. Young and M.J. Guiltinan (2003) Stable transformation of Theobroma cacao L. and influence of matrix attachment regions on GFP expression. Plant Cell Reports 21, 872-883.
85. F. Meins, Jr. (2000) RNA degradation and models for post-transcriptional gene-silencing. Plant Molecular Biology 43, 261-273.
86. S. Melquist and J. Bender (2003) Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis. Genes and Development 17, 2036-2047.
87. N. Mendu, M. Massel and S. Spiker (2001) Increasing loop domain size does not diminish effects of matrix attachment regions on transgene expression in tobacco cells culture. FEBS Letters 496, 66-67.
88. M.F. Mette, J. vanderWinden, M.A. Matzke and A.J.M. Matzke (1999) Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. The EMBO Journal 18, 241-248.
89. P. Meyer (2000) Transcriptional transgene silencing and chromatin components. Plant Molecular Biology 43, 221-234.
90. P. Meyer, F. Linn, I. Heidmann, H. Meyer, I. Niedenhof and H. Saedler (1992) Endogenous and environmental factors influence 35S promoter methylation of a maize A1 gene construct in transgenic petunia and its colour phenotype. Molecular and General Genetics 231, 345-352.
91. P. Meyer and H. Saedler (1996) Homology-dependent gene silencing in plants. Annual Review of Plant Physiology and Plant Molecular Biology 47, 23-48.
92. S.M. Michalowski, G.C. Allen, G.E. Hall, W.F. Thompson and S. Spiker (1999) Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants. Biochemistry 38, 12795-12804.
93. I. Mitsuhara, N. Shirasawa-Seo, T. Iwai, S. Nakamura, R. Honkura and Y. Ohashi (2002) Release from post-transcriptional gene silencing by cell proliferation in transgenic tobacco plants: possible mechanism for noninheritance of the silencing. Genetics 160, 343-352.
94. O. Mittelsten Scheid and J. Paszkowski (2000) Transcriptional gene silencing mutants. Plant Molecular Biology 43, 235-241.
95. A. Miura, S. Yonebayashi, K.Watanabe, T. Toyama, H. Shimada and T. Kakutani (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411, 212-214.
96. L. Mlynárová, A. Hricova, A. Loonen and J.P. Nap (2003) The presence of a chromatin boundary appears to shield a transgene in tobacco from RNA silencing. The Plant Cell 15, 2203-2217.
97. L. Mlynárová, R.C. Jansen, A.J. Conner, W.J. Stiekema and J.P. Nap (1995) The MAR-mediated reduction in position effect can be uncoupled from copy number-dependent expression in transgenic plants. The Plant Cell 7, 599-609.
98. L. Mlynárová, A. Loonen, J. Heldens, et al. (1994) Reduced position effect in mature transgenic plants conferred by the chicken lysozyme matrix-associated region. The Plant Cell 6, 417-426.
99. L. Mlynárová, A. Loonen, E. Mietkiewska, R.C. Jansen and J.P. Nap (2002) Assembly of two transgenes in an artificial chromatin domain gives highly coordinated expression in tobacco. Genetics 160, 727-740.
100. J.B. Morel, P. Mourrain, C. Beclin and H. Vaucheret (2000) DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis. Current Biology 10, 1591-1594.
101. M.R. Motamedi, A. Verdel, S.U. Colmenares, S.A. Gerber, S.P. Gygi and D. Moazed (2004) Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789-802.
102. P. Mourrain, C. Beclin, T. Elmayan, et al. (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101, 533-542.
103. N. Muangsan, C. Beclin, H. Vaucheret and D. Robertson (2004) Geminivirus VIGS of endogenous genes requires SGS2/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants. The Plant Journal 38, 1004-1014.
104. A. Muller, M. Marins, Y. Kamisugi and P. Meyer (2002) Analysis of hypermethylation in the RPS element suggests a signal function for short inverted repeats in de novo methylation. Plant Molecular Biology 48, 383-399.
105. M.W.M. Muskens, A.P.A. Vissers, J.N.M. Mol and J.M. Kooter (2000) Role of inverted DNA repeats in transcriptional and post-transcriptional gene silencing. Plant Molecular Biology 43, 243-260.
106. S. Nagaya, K. Kato, Y. Ninomiya, et al. (2005) Expression of randomly integrated single complete copy transgenes does not vary in Arabidopsis thaliana. Plant and Cell Physiology 46, 438-444.
107. S.J. Namciu, R.D. Friedman, M.D. Marsden, L.M. Sarausad, C.L. Jasoni and R.E. Fournier (2004) Sequence organization and matrix attachment regions of the human serine protease inhibitor gene cluster at 14q32.1. Mammalian Genome 15, 162-178.
108. C. Napoli, C. Lemieux and R. Jorgensen (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. The Plant Cell 2, 279-289.
109. F. Neuhuber, Y.D. Park, A.J.M. Matzke and M.A. Matzke (1994) Susceptibility of transgene loci to homology-dependent gene silencing. Molecular and General Genetics 244, 230-241.
110. J. Nickerson (2001) Experimental observations of a nuclear matrix. Journal of Cell Science 114, 463-474.
111. K. Noma, T. Sugiyama, H. Cam, et al. (2004) RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nature Genetics 36, 1174-1180.
112. W. Nowak, M. Gawlowska, A. Jarmolowski and J. Augustyniak (2001) Effect of nuclear matrix attachment regions on transgene expression in tobacco plants. Acta Biochimica Polonica 48, 637-646.
113. J.T. Odell and E. Krebbers (1998) Enhanced transgene expression in a population of monocot cells employing scaffold attachment regions. World Patent Office, World Patent, Dupont.
114. S.J. Oh, J.S. Jeong, E.H. Kim, et al. (2005) Matrix attachment region from the chicken lysozyme locus reduces variability in transgene expression and confers copy number-dependence in transgenic rice plants. Plant Cell Reports 24, 145-154.
115. M. Pal-Bhadra, B.A. Leibovitch, S.G. Gandhi, et al. (2004) Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303, 669-672.
116. X. Pan, Y. Li and L. Stein (2005) Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology 137, 168-175.
117. Y.D. Park, I. Papp, E.A. Moscone, et al. (1996) Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity. The Plant Journal 9, 183-194.
118. J.S. Parker, S.M. Roe and D. Barford (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. The EMBO Journal 23, 4727-4737.
119. A. Pecinka, N. Kato, A. Meister, A.V. Probst, I. Schubert and E. Lam (2005) Tandem repetitive transgenes and fluorescent chromatin tags alter local interphase chromosome arrangement in Arabidopsis thaliana. Journal of Cell Science 118, 3751-3758.
120. T. Pederson (1998) Thinking about a nuclear matrix. Journal of Molecular Biology 277, 147-159.
121. T. Pederson (2000) Half a century of 'the nuclear matrix'. Molecular Biology of the Cell 11, 799-805.
122. K. Petersen, R. Leah, S. Knudsen and V. Cameron-Mills (2002) Matrix attachment regions (MARs) enhance transformation frequencies and reduce variance of transgene expression in barley. Plant Molecular Biology 49, 45-58.
123. L. Phi-Van and W.H. Strätling (1996) Dissection of the ability of the chicken lysozyme gene 5′ matrix attachment region to stimulate transgene expression and to dampen position effects. Biochemistry 35, 10735-10742.
124. D. Pontier, G. Yahubyan, D. Vega, et al. (2005) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes and Development 19, 2030-2040.
125. A.V. Probst, P.F. Fransz, J. Paszkowski and O. Mittelsten Scheid (2003) Two means of transcriptional reactivation within heterochromatin. The Plant Journal 33, 743-749.
126. Q.D. Que, H.Y. Wang, J.J. English and R.A. Jorgensen (1997) The frequency and degree of cosuppression by sense chalcone synthase transgenes are dependent on transgene promoter strength and are reduced by premature nonsense codons in the transgene coding sequence. The Plant Cell 9, 1357-1368.
127. S. Rudd, M. Frisch, K. Grote, B.C. Meyers, K. Mayer and T. Werner (2004) Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiology 135, 715-722.
128. F. Schöffl, G. Schröder, M. Kliem and M. Rieping (1993) An SAR-sequence containing 395 bp-DNA fragment mediates enhanced, gene-dosage-correlated expression of a chimaeric heat shock gene in transgenic tobacco plants. Transgenic Research 2, 93-100.
129. V. Schramke, D.M. Sheedy, A.M. Denli, et al. (2005) RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature 435, 1275-1279.
130. D. Schubert, B. Lechtenberg, A. Forsbach, M. Gils, S. Bahadur and R. Schmidt (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.
131. K. Shimizu, M. Takahashi, N. Goshima, S. Kawakami, K. Irifune and H. Morikawa (2001) Presence of an SAR-like sequence in junction regions between an introduced transgene and genomic DNA of cultured tobacco cells: its effect on transformation frequency. The Plant Journal 26, 375-384.
132. L. Sidorenko, W. Bruce, S. Maddock, et al. (2003) Functional analysis of two matrix attachment region (MAR) elements in transgenic maize plants. Transgenic Research 12, 137-154.
133. T. Sijen, I. Vijn, A. Rebocho, et al. (2001) Transcriptional and posttranscriptional gene silencing are mechanistically related. Current Biology 11, 436-440.
134. G.B. Singh, J.A. Kramer and S.A. Krawetz (1997) Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Research 25, 1419-1425.
135. R.K. Slotkin, M. Freeling and D. Lisch (2005) Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nature Genetics 37, 641-644.
136. M. Stam, R. de Bruin, S. Kenter, et al. (1997a) Post-transcriptional silencing of chalcone synthase in petunia by inverted transgene repeats. The Plant Journal 12, 63-82.
137. M. Stam and O. Mittelsten Scheid (2005) Paramutation: an encounter leaving a lasting impression. Trends in Plant Science 10, 283-290.
138. M. Stam, J.N.M. Mol and J.M. Kooter (1997b) The silence of genes in transgenic plants. Annals of Botany 79, 3-12.
139. M. Stam, A. Viterbo, J.N.M. Mol and J.M. Kooter (1998) Position-dependent methylation and transcriptional silencing of transgenes in inverted T-DNArepeats: implications for posttranscriptional silencing of homologous host genes in plants. Molecular and Cellular Biology 18, 6165-6177.
140. A. Steimer, P. Amedeo, K. Afsar, P. Fransz, O. Mittelsten Scheid and J. Paszkowski (2000) Endogenous targets of transcriptional gene silencing in Arabidopsis. The Plant Cell 12, 1165-1178.
141. A. Stief, D.M. Winter, W.H. Strätling and A.E. Sippel (1989) A nuclear DNA attachment element mediates elevated and position-independent gene activity. Nature 341, 343-345.
142. P.A. Stoutjesdijk, S.P. Singh, Q. Liu, C.J. Hurlstone, P.A. Waterhouse and A.G. Green (2002) hpRNA-mediated targeting of the Arabidopsis FAD2 gene gives highly efficient and stable silencing. Plant Physiology 129, 1723-1731.
143. M. Tariq, Y. Habu and J. Paszkowski (2002) Depletion of MOM1 in non-dividing cells of Arabidopsis plants releases transcriptional gene silencing. EMBO Reports 3, 951-955.
144. M. Ten Lohuis, A. Muller, I. Heidmann, I. Niedenhof and P. Meyer (1995) A repetitive DNA fragment carrying a hot spot for de novo DNA methylation enhances expression variegation in tobacco and petunia. The Plant Journal 8, 919-932.
145. Y. Tomari and P.D. Zamore (2005) Perspective: machines for RNAi. Genes and Development 19, 517-529.
146. F. Torney, A. Partier, V. Says-Lesage, I. Nadaud, P. Barret and M. Beckert (2004) Heritable transgene expression pattern imposed onto maize ubiquitin promoter by maize adh-1 matrix attachment regions: tissue and developmental specificity in maize transgenic plants. Plant Cell Reports 22, 931-938.
147. M.A. Turnage, N. Muangsan, C.G. Peele and D. Robertson (2002) Geminivirus-based vectors for gene silencing in Arabidopsis. The Plant Journal 30, 107-114.
148. B. Ülker, G.C. Allen, W.F. Thompson, S. Spiker and A.K. Weissinger (1999) A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants. The Plant Journal 18, 253-263.
149. P. Vain, V.A. James, B. Worland and J.W. Snape (2002) Transgene behaviour across two generations in a large random population of transgenic rice plants produced by particle bombardment. Theoretical and Applied Genetics 105, 878-889.
150. P. Vain, B. Worland, A. Kohli, et al. (1999) Matrix attachment regions increase transgene expression levels and stability in transgenic rice plants and their progeny. The Plant Journal 18, 233-242.
151. F.E. Vaistij, L. Jones and D.C. Baulcombe (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.
152. R. Van Blokland, N. Van der Geest, J.N.M. Mol and J.M. Kooter (1994) Transgene-mediated suppression of chalcone synthase expression in petunia hybrida results from an increase in RNA turnover. The Plant Journal 6, 861-877.
153. A.H.M. Van der Geest, G.E. Hall, S. Spiker and T.C. Hall (1994) The beta-phaseolin gene is flanked by matrix attachment regions. The Plant Journal 6, 413-423.
154. A.H.M. Van der Geest, M.E. Welter, A.T. Woosley, et al. (2004) A short synthetic MAR positively affects transgene expression in rice and Arabidopsis. Plant Biotechnology Journal 2, 13-26.
155. A.R. van der Krol, L.A. Mur, M. Beld, J.N.M. Mol and A.R. Stuitje (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.
156. W. Van Leeuwen, L. Mlynárová, J.P. Nap, L.H. van der Plas and A.R. van der Krol (2001) The effect of MAR elements on variation in spatial and temporal regulation of transgene expression. Plant Molecular Biology 47, 543-554.
157. H. Vaucheret, T. Elmayan, D. Thierry, et al. (1998) Flank matrix attachment regions (MARs) from chicken, bean, yeast or tobacco do not prevent homology-dependent trans-silencing in transgenic tobacco plants. Molecular and General Genetics 259, 388-392.
158. K.J. Venken and H.J. Bellen (2005) Emerging technologies for gene manipulation in Drosophila melanogaster. Nature Reviews Genetics 6, 167-178.
159. D. Verma, M. Verma, M. Dey, R.K. Jain and R. Wu (2005) Molecular dissection of the tobacco Rb7 matrix attachment region (MAR): effect of 5′ half on gene expression in rice. Plant Science 169, 704-711.
160. T. Volpe, V. Schramke, G.L. Hamilton, et al. (2003) RNA interference is required for normal centromere function in fission yeast. Chromosome Research 11, 137-146.
161. T.A. Volpe, C. Kidner, I.M. Hall, G. Teng, S.I. Grewal, and R.A. Martienssen (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833-1837.
162. M.C. Walters, W. Magis, S. Fiering, et al. (1996) Transcriptional enhancers act in cis to suppress position-effect variegation. Genes and Development 10, 185-195.
163. M. Wassenegger (2005) The role of the RNAi machinery in heterochromatin formation. Cell 122, 13-16.
164. S.V. Wesley, C.A. Helliwell, N.A. Smith, et al. (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. The Plant Journal 27, 581-590.
165. A.P. Wolffe (1997) Transcription control: repressed repeats express themselves. Current Biology 7, R796-R798.
166. Y.-Y. Xu, X.-M.Wang, J. Li, et al. (2005) Activation of theWUSgene induces ectopic initiation of floral meristems on mature stem surface in Arabidopsis thaliana. Plant Molecular Biology 57, 773-784.
167. H. Xue, Y.T. Yang, C.A. Wu, G.D. Yang, M.M. Zhang and C.C. Zheng (2005) TM2, a novel strong matrix attachment region isolated from tobacco, increases transgene expression in transgenic rice calli and plants. Theoretical and Applied Genetics 110, 620-627.
168. S.Y. Yoo, K. Bomblies, S.K. Yoo, et al. (2005) The 35S promoter used in a selectable marker gene of a plant transformation vector affects the expression of the transgene. Planta 221, 523-530.
169. M. Yoshikawa, A. Peragine, M.Y. Park and R.S. Poethig (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes and Development 19, 2164-2175.