Endogenous targets of transcriptional gene silencing in Arabidopsis

Plant Cell

Volumn 12, Issue 7, 2000, Pages 1165-1178

  Steimer, Andrea ^a   Amedeo, Paolo ^a   Afsar, Karin ^a   Fransz, Paul ^b   Scheid, Ortrun Mittelsten ^a   Paszkowski, Jerzy ^a  

^a FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH   (Switzerland)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CLONE; COMPLEMENTARY DNA; FOREIGN GENE; GENE INACTIVATION; GENE SILENCING; GENETIC REGULATION; MUTANT; REPETITIVE DNA; RETROPOSON; RNA SYNTHESIS; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION; TRANSGENE; WILD RELATIVE;

ARABIDOPSIS; EMBRYOPHYTA;

EID: 0033869467     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.12.7.1165     Document Type: Article

References (70)

1. Albinsky, D., Masson, J.E., Bogucki, A., Afsar, K., Vass, I., Nagy, F., and Paszkowski, J. (1999). Plant responses to genotoxic stress are linked to an ABA/salinity signaling pathway. Plant J. 17, 73-82.
2. Amedeo, P., Habu, Y., Afsar, K., Mittelsten Scheid, O., and Paszkowski, J. (2000). Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405, 203-206.
3. Bender, J., and Fink, G.R. (1995). Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83, 725-734.
4. Bevan, M., Bancroft, I., Mewes, H.W., Martienssen, R., and McCombie, R. (1999). Clearing a path through the jungle: Progress in Arabidopsis genomics. Bioessays 21, 110-120.
5. Brettell, R.I. and Dennis, E.S. (1991). Reactivation of a silent Ac following tissue culture is associated with heritable alterations in its methylation pattern. Mol. Gen. Genet. 229, 365-372.
6. Cambareri, E.B., Aisner, R., and Carbon, J. (1998). Structure of the chromosome VII centromere region in Neurospora crassa: Degenerate transposons and simple repeats. Mol. Cell. Biol. 18, 5465-5477.
7. Chen, Z.J., and Pikaard, C.S. (1997). Epigenetic silencing of RNA polymerase I transcription: A role for DNA methylation and histone modification in nucleolar dominance. Genes Dev. 11, 2124-2136.
8. Church, G.M., and Gilbert, W. (1984). Genomic sequencing. Proc. Natl. Acad. Sci. USA 81, 1991-1995.
9. Copenhaver, G.P., and Preuss, D. (1999). Centromeres in the genomic era: Unraveling paradoxes. Curr. Opin. Plant Biol. 2, 104-108.
10. Copenhaver, G.P., et al. (1999). Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286, 2468-2474.
11. Creusot, F., et al. (1995). The CIC library: A large insert YAC library for genome mapping in Arabidopsis thaliana. Plant J. 8, 763-770.
12. Csink, A.K., and Henikoff, S. (1998). Something from nothing: The evolution and utility of satellite repeats. Trends Genet. 14, 200-204.
13. Cubas, P., Vincent, C., and Coen, E. (1999). An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157-161.
14. Dellaporta, S.L., Wood, J., and Hicks, J.B. (1983). A plant DNA minipreparation. Version II. Plant Mol. Biol. Rep. 1, 19-21.
15. Depicker, A., and Van Montagu, M. (1997). Post-transcriptional gene silencing in plants. Curr. Opin. Cell Biol. 9, 373-382.
16. Diatchenko, L., Lau, Y.-F., Campbell, A.P., Chenchik, A., Moqadam, F., Huang, B., Lukyanov, S., Lukyanov, K., Gurskaya, N., Sverdlov, E., and Siebert, P.D. (1996). Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93, 6025-6030.
17. Doolittle, R.F., Feng, D.F., Johnson, M.S., and McClure, M.A. (1989). Origins and evolutionary relationships of retroviruses. Q. Rev. Biol. 64, 1-30.
18. Feinberg, A.P., and Vogelstein, B. (1983). A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132, 6-13.
19. Finnegan, E.J., Peacock, W.J., and Dennis, E.S. (1996). Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. USA 93, 8449-8454.
20. Finnegan, E.J., Genger, R.K., Peacock, W.J., and Dennis, E.S. (1998). DNA methylation in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49, 223-247.
21. Fransz, P., Armstrong, S., Alonso-Blanco, C., Fischer, T.C., Torres-Ruiz, R.A., and Jones, G.H. (1998). Cytogenetics for the model system Arabidopsis thaliana. Plant J. 136, 867-876.
22. Fransz, P.F., Armstrong, S., de Jong, J.H., Parnell, L.D., van Drunen, C., Dean, C., Zabel, P., Bisseling, T., and Jones, G.H. (2000). Integrated cytogenetic map of chromosome arm 4S of A. thaliana: Structural organization of heterochromatic knob and centromere region. Cell 100, 367-376.
23. Furner, I.J., Sheikh, M.A., and Collett, C.E. (1998). Gene silencing and homology-dependent gene silencing in Arabidopsis: Genetic modifiers and DNA methylation. Genetics 149, 651-662.
24. Gartler, S.M., Goldstein, L., Tyler-Freer, S.E., and Hansen, R.S. (1999). The timing of XIST replication: Dominance of the domain. Hum. Mol. Gen. 8, 1085-1089.
25. Goodall, G.J., Wiebauer, K., and Filipowicz, W. (1990). Analysis of pre-mRNA processing in transfected plant protoplasts. Methods Enzymol. 181, 148-161.
26. Goodrich, J., Puangsomlee, P., Martin, M., Long, D., Meyerowitz, E.M., and Coupland, G. (1997). A polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 386, 44-51.
27. Grant, S.R. (1999). Dissecting the mechanisms of posttranscriptional gene silencing: Divide and conquer. Cell 96, 303-306.
28. Gregory, P.D., and Hoerz, W. (1998). Chromatin and transcription - How transcription factors battle with a repressive chromatin environment. Eur. J. Biochem. 251, 9-18.
29. Haizel, T., Merkle, T., Pay, A., Fejes, E., and Nagy, F. (1997). Characterization of proteins that interact with the GTP-bound form of the regulatory GTPase Ran in Arabidopsis. Plant J. 11, 93-103.
30. Henikoff, S. (1998). Conspiracy of silence among repeated transgenes. Bioessays 20, 532-535.
31. Hirochika, H. (1993). Activation of tobacco retrotransposons during tissue culture. EMBO J. 12, 2521-2528.
32. Hirochika, H., Sugimoto, K., Otsuki, Y., Tsugawa, H., and Kanda, M. (1996). Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl. Acad. Sci. USA 93, 7783-7788.
33. Hirochika, H., Okamoto, H., and Kakutani, T. (2000). Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12, 357-369.
34. Jacobsen, S.E., and Meyerowitz, E.M. (1997). Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277, 1100-1103.
35. Jeddeloh, J.A., Bender, J., and Richards, E.J. (1998). The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 12, 1714-1725.
36. Jeddeloh, J.A., Stokes, T.L., and Richards, E. (1999). Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 22, 94-97.
37. Kakutani, T., Jeddeloh, J.A., Flowers, S.K., Munakata, K., and Richards, E. (1996). Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. USA 93, 12406-12411.
38. Kakutani, T., Munakata, K., Richards, E.J., and Hirochika, H. (1999). Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151, 831-838.
39. Konieczny, A., Voytas, D.F., Cummings, M.P., and Ausubel, F.M. (1991). A superfamily of Arabidopsis thaliana retrotransposons. Genetics 127, 801-809.
40. Lin, X.Y., et al. (1999). Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402, 761-768.
41. Liu, C.-M., and Meinke, D.W. (1998). The titan mutants of Arabidopsis are disrupted in mitosis and cell cycle control during seed development. Plant J. 16, 21-31.
42. Maluszynka, J., and Heslop-Harrison, J.S. (1991). Localization of tandemly repeated DNA sequences in Arabidopsis thaliana. Plant J. 1, 159-166.
43. Marahrens, Y. (1999). X-inactivation by chromosomal pairing events. Genes Dev. 13, 2624-2632.
44. Martienssen, R. (1998). Chromosomal imprinting in plants. Curr. Opin. Genet. Dev. 8, 240-244.
45. Martinez-Zapater, J.M., Estelle, M.A., and Sommerville, C.R. (1986). A highly repeated DNA sequence in Arabidopsis thaliana. Mol. Gen. Genet. 204, 417-423.
46. Masson, J., and Paszkowski, J. (1992). The culture response of Arabidopsis thaliana protoplasts is determined by the growth conditions of the donor plants. Plant J. 2, 829-833.
47. Matzke, M.A., and Matzke, A.J.M. (1998). Epigenetic silencing of plant transgenes as a consequence of diverse cellular defence responses. Cell Mol. Life Sci. 54, 94-103.
48. Matzke, M.A., Matzke, A.J.M., and Eggleston, W.B. (1996). Paramutation and transgene silencing: A common response to invasive DNA? Trends Plant Sci. 1, 382-388.
49. May, M.J., and Leaver, C.J. (1993). Oxidative stimulation of glutathione synthesis in Arabidopsis thaliana suspension cultures. Plant Physiol. 103, 621-627.
50. Mayer, K., et al. (1999). Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402, 769-777.
51. McCombie, W.R., et al. (2000). The complete sequence of a heterochromatic island from a higher eukaryote. Cell 100, 377-386.
52. Meyer, P. (1996). Repeat-induced gene silencing: Common mechanisms in plants and fungi. Biol. Chem. Hoppe-Seyler 377, 87-95.
53. Mittelsten Scheid, O., Paszkowski, J., and Potrykus, I. (1991). Reversible inactivation of a transgene in Arabidopsis thaliana. Mol. Gen. Genet. 228, 104-112.
54. Mittelsten Scheid, O., Afsar, K., and Paszkowski, J. (1998). Release of epigenetic gene silencing by trans-acting mutations in Arabidopsis. Proc. Natl. Acad. Sci. USA 95, 632-637.
55. Pardue, M.L., Danilevskaya, O.N., Traverse, K.L., and Lowenhaupt, K. (1997). Evolutionary links between telomeres and transposable elements. Genetica 100, 73-84.
56. Peleman, J., Cottyn, B., Van Camp, W., Van Montagu, M., and Inze, D. (1991). Transient occurrence of extrachromosomal DNA of an Arabidopsis thaliana transposon-like element, Tat1. Proc. Natl. Acad. Sci. USA 88, 3618-3622.
57. Pélissier, T., Tutois, S., Deragon, J.M., Tourmente, S., Genestier, S., and Picard, G. (1995). Athila, a new retroelement from Arabidopsis thaliana. Plant Mol. Biol. 29, 441-452.
58. Pélissier, T., Tutois, S., Tourmente, S., Deragon, J.M., and Picard, G. (1996). DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica 97, 141-151.
59. Phillips, R.L., Kaeppler, S.M., and Olhoft, P. (1994). Genetic instability of plant tissue cultures: Breakdown of normal controls. Proc. Natl. Acad. Sci. USA 91, 5222-5226.
60. Presting, G.G., Malysheva, L., Fuchs, J., and Schubert, I.Z. (1998). A TY3/GYPSY retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J. 16, 721-728.
61. Revenkova, E., Masson, J., Koncz, C., Afsar, K., Jakovleva, L., and Paszkowski, J. (1999). Involvement of Arabidopsis thaliana ribosomal protein S27 in mRNA degradation triggered by genotoxic stress. EMBO J. 18, 490-499.
62. Richards, E.J. (1997). DNA methylation and plant development. Trends Genet. 13, 319-323.
63. Ross, K., Fransz, P., and Jones, G.H. (1996). A light microscopic atlas of meiosis in Arabidopsis thaliana. Chromosome Res. 4, 507-516.
64. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press).
65. Selker, E.U. (1997). Epigenetic phenomena in filamentous fungi: Useful paradigms or repeat-induced confusions? Trends Genet. 13, 296-301.
66. Stam, M., Mol, J.N., and Kooter, J.M. (1997). The silence of genes in transgenic plants. Ann. Bot. 79, 3-12.
67. Vaucheret, H., Beclin, C., Elmayan, T., Feuerbach, F., Godon, C., Morel, J.-B., Mourrain, P., Palaqui, J.-C., and Vernhettes, S. (1998). Transgene-induced gene silencing in plants. Plant J. 16, 651-659.
68. von Stein, O.D., Thies, W.-G., and Hofmann, M. (1997). A high throughput screening for rarely transcribed differentially expressed genes. Nucleic Acids Res. 25, 2598-2602.
69. Vongs, A., Kakutani, T., Martienssen, R.A., and Richards, E.J. (1993). Arabidopsis thaliana DNA methylation mutants. Science 260, 1926-1928.
70. Wright, D.A., and Voytas, D.F. (1998). Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/ gypsy retrotransposons that encode envelope-like proteins. Genetics 149, 703-715.