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For: Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they're down. Genome Biol 2004;5:249. [PMID: 15575975 PMCID: PMC545787 DOI: 10.1186/gb-2004-5-12-249] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
Number Cited by Other Article(s)
1
Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife 2021;10:72676. [PMID: 34850679 PMCID: PMC8828055 DOI: 10.7554/elife.72676] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/30/2021] [Indexed: 11/27/2022]  Open
2
Hendrix B, Hoffer P, Sanders R, Schwartz S, Zheng W, Eads B, Taylor D, Deikman J. Systemic GFP silencing is associated with high transgene expression in Nicotiana benthamiana. PLoS One 2021;16:e0245422. [PMID: 33720987 PMCID: PMC7959375 DOI: 10.1371/journal.pone.0245422] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/21/2021] [Indexed: 12/28/2022]  Open
3
Markova DN, Mason-Gamer RJ. Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae. BMC Evol Biol 2017;17:178. [PMID: 28774284 PMCID: PMC5543537 DOI: 10.1186/s12862-017-1028-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 07/26/2017] [Indexed: 11/10/2022]  Open
4
Susek K, Braszewska-Zalewska A, Bewick AJ, Hasterok R, Schmitz RJ, Naganowska B. Epigenomic diversification within the genus Lupinus. PLoS One 2017;12:e0179821. [PMID: 28640886 PMCID: PMC5480990 DOI: 10.1371/journal.pone.0179821] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/05/2017] [Indexed: 12/23/2022]  Open
5
Small RNAs: Master Regulators of Epigenetic Silencing in Plants. PLANT EPIGENETICS 2017. [DOI: 10.1007/978-3-319-55520-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
6
Mlinarec J, Franjević D, Harapin J, Besendorfer V. The impact of the Tekay chromoviral elements on genome organisation and evolution of Anemone s.l. (Ranunculaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2016;18:332-347. [PMID: 26370195 DOI: 10.1111/plb.12393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
7
Maurer-Alcalá XX, Katz LA. An epigenetic toolkit allows for diverse genome architectures in eukaryotes. Curr Opin Genet Dev 2015;35:93-9. [PMID: 26649755 DOI: 10.1016/j.gde.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 02/04/2023]
8
de Meaux J, Pecinka A. The Arabidopsis genus: An emerging model to elucidate the molecular basis of interspecific differences in transposable element activity. Mob Genet Elements 2014;2:142-144. [PMID: 23061020 PMCID: PMC3463470 DOI: 10.4161/mge.21111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
9
Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. TRENDS IN PLANT SCIENCE 2014;19:320-6. [PMID: 24618094 DOI: 10.1016/j.tplants.2014.01.014] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 05/06/2023]
10
Ungerer MC, Kawakami T. Transcriptional dynamics of LTR retrotransposons in early generation and ancient sunflower hybrids. Genome Biol Evol 2013;5:329-37. [PMID: 23335122 PMCID: PMC3590766 DOI: 10.1093/gbe/evt006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
11
Nosaka M, Ishiwata A, Shimizu-Sato S, Ono A, Ishimoto K, Noda Y, Sato Y. The copy number of rice CACTA DNA transposons carrying MIR820 does not correlate with MIR820 expression. PLANT SIGNALING & BEHAVIOR 2013;8:25169. [PMID: 23733074 PMCID: PMC3999066 DOI: 10.4161/psb.25169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 05/21/2023]
12
Nosaka M, Ono A, Ishiwata A, Shimizu-Sato S, Ishimoto K, Noda Y, Sato Y. Expression of the rice microRNA miR820 is associated with epigenetic modifications at its own locus. Genes Genet Syst 2013;88:105-12. [DOI: 10.1266/ggs.88.105] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
13
Nosaka M, Itoh JI, Nagato Y, Ono A, Ishiwata A, Sato Y. Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice. PLoS Genet 2012;8:e1002953. [PMID: 23028360 PMCID: PMC3459959 DOI: 10.1371/journal.pgen.1002953] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 07/31/2012] [Indexed: 11/18/2022]  Open
14
Lee TF, Gurazada SGR, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC. RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 2012;7:781-95. [PMID: 22647529 PMCID: PMC3679228 DOI: 10.4161/epi.20290] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
15
He F, Zhang X, Hu JY, Turck F, Dong X, Goebel U, Borevitz JO, de Meaux J. Widespread interspecific divergence in cis-regulation of transposable elements in the Arabidopsis genus. Mol Biol Evol 2011;29:1081-91. [PMID: 22086904 DOI: 10.1093/molbev/msr281] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
16
Lisch D, Bennetzen JL. Transposable element origins of epigenetic gene regulation. CURRENT OPINION IN PLANT BIOLOGY 2011;14:156-61. [PMID: 21444239 DOI: 10.1016/j.pbi.2011.01.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 01/22/2011] [Indexed: 05/07/2023]
17
Kawakami T, Dhakal P, Katterhenry AN, Heatherington CA, Ungerer MC. Transposable element proliferation and genome expansion are rare in contemporary sunflower hybrid populations despite widespread transcriptional activity of LTR retrotransposons. Genome Biol Evol 2011;3:156-67. [PMID: 21282712 PMCID: PMC3048363 DOI: 10.1093/gbe/evr005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
18
Natural history of eukaryotic DNA methylation systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011;101:25-104. [PMID: 21507349 DOI: 10.1016/b978-0-12-387685-0.00002-0] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
19
Qüesta JI, Walbot V, Casati P. Mutator transposon activation after UV-B involves chromatin remodeling. Epigenetics 2010;5:352-63. [PMID: 20421734 DOI: 10.4161/epi.5.4.11751] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
20
Volff JN. Cellular Genes Derived from Gypsy/Ty3 Retrotransposons in Mammalian Genomes. Ann N Y Acad Sci 2009;1178:233-43. [PMID: 19845640 DOI: 10.1111/j.1749-6632.2009.05005.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
21
Feng J, Naiman DQ, Cooper B. Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing. MOLECULAR BIOSYSTEMS 2009;5:1679-87. [PMID: 19452047 DOI: 10.1039/b903031j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
22
Baubec T, Pecinka A, Rozhon W, Mittelsten Scheid O. Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009;57:542-54. [PMID: 18826433 PMCID: PMC2667684 DOI: 10.1111/j.1365-313x.2008.03699.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/09/2008] [Accepted: 09/18/2008] [Indexed: 05/21/2023]
23
Uchiyama T, Saito Y, Kuwabara H, Fujino K, Kishima Y, Martin C, Sano Y. Multiple regulatory mechanisms influence the activity of the transposon, Tam3, of Antirrhinum. THE NEW PHYTOLOGIST 2008;179:343-355. [PMID: 19086175 DOI: 10.1111/j.1469-8137.2008.02477.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
24
Gehring M, Henikoff S. DNA methylation and demethylation in Arabidopsis. THE ARABIDOPSIS BOOK 2008;6:e0102. [PMID: 22303233 PMCID: PMC3243302 DOI: 10.1199/tab.0102] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
25
Vaillant I, Tutois S, Jasencakova Z, Douet J, Schubert I, Tourmente S. Hypomethylation and hypermethylation of the tandem repetitive 5S rRNA genes in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008;54:299-309. [PMID: 18208523 DOI: 10.1111/j.1365-313x.2008.03413.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
26
Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 2008;177:1975-85. [PMID: 18073417 DOI: 10.1534/genetics.107.080234] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
27
Chen S, Li X. Molecular characterization of the first intact Transib transposon from Helicoverpa zea. Gene 2008;408:51-63. [DOI: 10.1016/j.gene.2007.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/06/2007] [Accepted: 10/12/2007] [Indexed: 01/10/2023]
28
Jiao Y, Deng XW. A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol 2007;8:R28. [PMID: 17326825 PMCID: PMC1852403 DOI: 10.1186/gb-2007-8-2-r28] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Revised: 12/18/2006] [Accepted: 02/27/2007] [Indexed: 12/20/2022]  Open
29
Navarre WW, McClelland M, Libby SJ, Fang FC. Silencing of xenogeneic DNA by H-NS--facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev 2007;21:1456-71. [PMID: 17575047 DOI: 10.1101/gad.1543107] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
30
Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu JK. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 2007;17:54-9. [PMID: 17208187 DOI: 10.1016/j.cub.2006.10.059] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 10/17/2006] [Accepted: 10/30/2006] [Indexed: 12/17/2022]
31
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 2006;39:61-9. [PMID: 17128275 DOI: 10.1038/ng1929] [Citation(s) in RCA: 921] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 10/24/2006] [Indexed: 11/09/2022]
32
Agius F, Kapoor A, Zhu JK. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci U S A 2006;103:11796-801. [PMID: 16864782 PMCID: PMC1544249 DOI: 10.1073/pnas.0603563103] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
33
Kapoor A, Agarwal M, Andreucci A, Zheng X, Gong Z, Hasegawa PM, Bressan RA, Zhu JK. Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA-methylation-independent manner in Arabidopsis. Curr Biol 2006;15:1912-8. [PMID: 16271867 DOI: 10.1016/j.cub.2005.09.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Revised: 09/01/2005] [Accepted: 09/02/2005] [Indexed: 12/01/2022]
34
Dong ZY, Wang YM, Zhang ZJ, Shen Y, Lin XY, Ou XF, Han FP, Liu B. Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006;113:196-205. [PMID: 16791687 DOI: 10.1007/s00122-006-0286-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 03/31/2006] [Indexed: 05/04/2023]
35
Navarre WW, Porwollik S, Wang Y, McClelland M, Rosen H, Libby SJ, Fang FC. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 2006;313:236-8. [PMID: 16763111 DOI: 10.1126/science.1128794] [Citation(s) in RCA: 545] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
36
Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol 2005;6:R90. [PMID: 16277745 PMCID: PMC1297646 DOI: 10.1186/gb-2005-6-11-r90] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 08/26/2005] [Accepted: 09/21/2005] [Indexed: 11/16/2022]  Open
37
Woodhouse MR, Freeling M, Lisch D. The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize. Genetics 2005;172:579-92. [PMID: 16219782 PMCID: PMC1456185 DOI: 10.1534/genetics.105.051383] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
38
Slotkin RK, Freeling M, Lisch D. Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet 2005;37:641-4. [PMID: 15908951 DOI: 10.1038/ng1576] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Accepted: 04/22/2005] [Indexed: 11/08/2022]
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