Bennetzen JL. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev. 2005;15:621–7.
Article
CAS
Google Scholar
Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol. 2015;16:519–32.
Article
CAS
Google Scholar
Zhang H, Lang Z, Zhu J-K. Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol. 2018;19:489.
Article
CAS
Google Scholar
Quadrana L, Bortolini Silveira A, Mayhew GF, LeBlanc C, Martienssen RA, Jeddeloh JA, et al. The Arabidopsis thaliana mobilome and its impact at the species level. eLife. 2016;5:e15716.
Article
Google Scholar
Zhou S, Liu X, Zhou C, Zhou Q, Zhao Y, Li G, et al. Cooperation between the H3K27me3 chromatin mark and non-CG methylation in epigenetic regulation. Plant Physiol. 2016;172:1131–41.
CAS
PubMed
PubMed Central
Google Scholar
Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell. 2008;135:635–48.
Article
CAS
Google Scholar
Fojtová M, Houdt HV, Depicker A, Kovarik A. Epigenetic switch from posttranscriptional to transcriptional silencing is correlated with promoter hypermethylation. Plant Physiol. 2003;133:1240–50.
Article
Google Scholar
Saze H, Kakutani T. Differentiation of epigenetic modifications between transposons and genes. Curr Opin Plant Biol. 2011;14:81–7.
Article
CAS
Google Scholar
Finnegan EJ, Peacock WJ, Dennis ES. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. PNAS. 1996;93:8449–54.
Article
CAS
Google Scholar
Jones L, Ratcliff F, Baulcombe DC. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr Biol. 2001;11:747–57.
Article
CAS
Google Scholar
Woo HR, Pontes O, Pikaard CS, Richards EJ. VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. Gene Dev. 2007;21:267–77.
Article
CAS
Google Scholar
Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, Caro E, et al. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell. 2012;151:167–80.
Article
CAS
Google Scholar
Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153:193–205.
Article
CAS
Google Scholar
Jackson JP, Lindroth AM, Cao X, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature. 2002;416:556–60.
Article
CAS
Google Scholar
Malagnac F, Bartee L, Bender J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J. 2002;21:6842–52.
Article
CAS
Google Scholar
Ebbs ML, Bartee L, Bender J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol. 2005;25:10507–15.
Article
CAS
Google Scholar
Ebbs ML, Bender J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell. 2006;18:1166–76.
Article
CAS
Google Scholar
Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, et al. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol. 2007;17:379–84.
Article
CAS
Google Scholar
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, et al. Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol Cell. 2014;55:495–504.
Article
CAS
Google Scholar
Stoddard CI, Feng S, Campbell MG, Liu W, Wang H, Zhong X, et al. A nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase. Mol Cell. 2019;73:73–83.e6.
Article
CAS
Google Scholar
Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292:2077–80.
Article
CAS
Google Scholar
Stroud H, Greenberg MVC, Feng S, Bernatavichute YV, Jacobsen SE. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell. 2013;152:352–64.
Article
CAS
Google Scholar
Bologna NG, Voinnet O. The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol. 2014;65:473–503.
Article
CAS
Google Scholar
Elvira-Matelot E, Martínez ÁE. Diversity of RNA silencing pathways in plants. Plant Gene Silenc Mech Appl. 2017;5:1–31.
Google Scholar
Zhong X, Du J, Hale CJ, Gallego-Bartolome J, Feng S, Vashisht AA, et al. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell. 2014;157:1050–60.
Article
CAS
Google Scholar
Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. RNA polymerase IV directs silencing of endogenous DNA. Science. 2005;308:118–20.
Article
CAS
Google Scholar
Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell. 2005;120:613–22.
Article
CAS
Google Scholar
Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, et al. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet. 2005;37:761–5.
Article
CAS
Google Scholar
Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi M-A, et al. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Gene Dev. 2005;19:2030–40.
Article
CAS
Google Scholar
Law JA, Vashisht AA, Wohlschlegel JA, Jacobsen SE. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet. 2011;7:e1002195.
Article
CAS
Google Scholar
Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AMS, et al. Polymerase-IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature. 2013;498:385–9.
Article
CAS
Google Scholar
Zhang H, Ma Z-Y, Zeng L, Tanaka K, Zhang C-J, Ma J, et al. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. PNAS. 2013;110:8290–5.
Article
CAS
Google Scholar
Blevins T, Podicheti R, Mishra V, Marasco M, Wang J, Rusch D, et al. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. eLife. 2015;4:e09591.
Article
Google Scholar
Li S, Vandivier LE, Tu B, Gao L, Won SY, Li S, et al. Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Res. 2015;25:235–45.
Article
CAS
Google Scholar
Zhai J, Bischof S, Wang H, Feng S, Lee T, Teng C, et al. A one precursor one siRNA model for Pol IV-dependent siRNA biogenesis. Cell. 2015;163:445–55.
Article
CAS
Google Scholar
Zhang Z, Liu X, Guo X, Wang X-J, Zhang X. Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing. Nat Plants. 2016;2:16049.
Article
CAS
Google Scholar
El-Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Gene Dev. 2007;21:2539–44.
Article
CAS
Google Scholar
Yang D-L, Zhang G, Tang K, Li J, Yang L, Huang H, et al. Dicer-independent RNA-directed DNA methylation in Arabidopsis. Cell Res. 2016;26:66–82.
Article
CAS
Google Scholar
Kuhlmann M, Mette MF. Developmentally non-redundant SET domain proteins SUVH2 and SUVH9 are required for transcriptional gene silencing in Arabidopsis thaliana. Plant Mol Biol. 2012;79:623–33.
Article
CAS
Google Scholar
Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, et al. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2014;507:124–8.
Article
CAS
Google Scholar
Liu Z-W, Shao C-R, Zhang C-J, Zhou J-X, Zhang S-W, Li L, et al. The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet. 2014;10:e1003948.
Article
Google Scholar
Marí-Ordóñez A, Marchais A, Etcheverry M, Martin A, Colot V, Voinnet O. Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet. 2013;45:1029–39.
Article
Google Scholar
Fultz D, Slotkin RK. Exogenous transposable elements circumvent identity-based silencing, permitting the dissection of expression-dependent silencing. Plant Cell. 2017;29:360–76.
Article
CAS
Google Scholar
Ye R, Chen Z, Lian B, Rowley MJ, Xia N, Chai J, et al. A Dicer-independent route for biogenesis of siRNAs that direct DNA methylation in Arabidopsis. Mol Cell. 2016;61:222–35.
Article
CAS
Google Scholar
Vaucheret H, Institut N de la RA. Promoter-dependent trans-inactivation in transgenic tobacco plants: kinetic aspects of gene silencing and gene reactivation. C R Acad Sci III. 1994:310–23.
Philips JG, Dudley KJ, Waterhouse PM, Hellens RP. The rapid methylation of T-DNAs upon agrobacterium inoculation in plant leaves. Front Plant Sci. 2019. https://doi.org/10.3389/fpls.2019.00312.
Article
PubMed
PubMed Central
Google Scholar
Xu C, Corces VG. Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites. Science. 2018;359:1166–70.
Article
CAS
Google Scholar
Nagata T, Nemoto Y, Hasezawa S. Tobacco BY-2 cell line as the “HeLa” cell in the cell biology of higher plants. In: Jeon KW, Friedlander M, editors. International review of cytology. Cambridge: Academic Press; 1992. p. 1–30. https://doi.org/10.1016/s0074-7696(08)62452-3.
Chapter
Google Scholar
Srba M, Černíková A, Opatrný Z, Fischer L. Practical guidelines for the characterization of tobacco BY-2 cell lines. Biol Plant. 2016;60:13–24.
Article
CAS
Google Scholar
Nocarova E, Fischer L. Cloning of transgenic tobacco BY-2 cells; an efficient method to analyse and reduce high natural heterogeneity of transgene expression. BMC Plant Biol. 2009;9:44.
Article
Google Scholar
Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, et al. The complex architecture and epigenomic impact of plant T-DNA insertions. PLoS Genet. 2019;15:e1007819.
Article
Google Scholar
Wroblewski T, Matvienko M, Piskurewicz U, Xu H, Martineau B, Wong J, et al. Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis. RNA. 2014;20:1987–99.
Article
CAS
Google Scholar
Grandbastien M-A, Spielmann A, Caboche M. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature. 1989;337:376.
Article
CAS
Google Scholar
Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M. Retrotransposons of rice involved in mutations induced by tissue culture. PNAS. 1996;93:7783–8.
Article
CAS
Google Scholar
Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, et al. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics. 2003;163:1109–22.
CAS
PubMed
PubMed Central
Google Scholar
Zabet NR, Catoni M, Prischi F, Paszkowski J. Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. Nucleic Acids Res. 2017;45:3777–84.
CAS
PubMed
PubMed Central
Google Scholar
Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biol. 2016;17:170.
Article
Google Scholar
Parent J-S, Bouteiller N, Elmayan T, Vaucheret H. Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing. Plant J. 2015;81:223–32.
Article
CAS
Google Scholar
Sijen T, Vijn I, Rebocho A, van Blokland R, Roelofs D, Mol JN, et al. Transcriptional and posttranscriptional gene silencing are mechanistically related. Curr Biol. 2001;11:436–40.
Article
CAS
Google Scholar
Čermák V, Fischer L. Pervasive read-through transcription of T-DNAs is frequent in tobacco BY-2 cells and can effectively induce silencing. BMC Plant Biol. 2018;18:252.
Article
Google Scholar
Křížová K, Depicker A, Kovařík A. Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture. Epigenetics. 2013;8:666–76.
Article
Google Scholar
Ford E, Grimmer MR, Stolzenburg S, Bogdanovic O, Mendoza A de, Farnham PJ, et al. Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation. 2017. http://bioRxiv.org/170506.
Matsunaga W, Shimura H, Shirakawa S, Isoda R, Inukai T, Matsumura T, et al. Transcriptional silencing of 35S driven-transgene is differentially determined depending on promoter methylation heterogeneity at specific cytosines in both plus- and minus-sense strands. BMC Plant Biol. 2019;19:24.
Article
Google Scholar
Johnson LM, Law JA, Khattar A, Henderson IR, Jacobsen SE. SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet. 2008;4:e1000280.
Article
Google Scholar
Jackel JN, Storer J, Coursey T, Bisaro D. Arabidopsis RNA polymerases IV and V are required to establish H3K9 methylation, but not cytosine methylation, on geminivirus chromatin. J Virol. 2016;90:7529–40.
Article
CAS
Google Scholar
Murashige T, Skoog F. A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant. 1962;15:473–97.
Article
CAS
Google Scholar
Davis SJ, Vierstra RD. Soluble, highly fluorescent variants of green fluorescent protein (GFP) for use in higher plants. Plant Mol Biol. 1998;36:521–8.
Article
CAS
Google Scholar
Duchoslav M, Fischer L. Parallel subfunctionalisation of PsbO protein isoforms in angiosperms revealed by phylogenetic analysis and mapping of sequence variability onto protein structure. BMC Plant Biol. 2015;15:133.
Article
Google Scholar
Motylová Š. The influence of RDR6 activity and mode of RNAi induction on dynamics and mechanism of silencing of the reporter GFP gene in tobacco cell line BY-2. Diploma thesis. Faculty of Science, Charles University. 2015. http://hdl.handle.net/20.500.11956/74403.
Zuo J, Niu Q-W, Chua N-H. An estrogen receptor-based transactivator XVE mediates highly inducible gene expression in transgenic plants. Plant J. 2000;24:265–73.
Article
CAS
Google Scholar
Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB, et al. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009;37:e45.
Article
CAS
Google Scholar
Nicot N, Hausman J-F, Hoffmann L, Evers D. Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot. 2005;56:2907–14.
Article
CAS
Google Scholar
Dvořáková L, Srba M, Opatrny Z, Fischer L. Hybrid proline-rich proteins: novel players in plant cell elongation? Ann Bot. 2012;109:453–62.
Article
Google Scholar
Tyč D, Nocarová E, Sikorová L, Fischer L. 5-Azacytidine mediated reactivation of silenced transgenes in potato (Solanum tuberosum) at the whole plant level. Plant Cell Rep. 2017;36:1311–22.
Article
Google Scholar
Bond DM, Baulcombe DC. Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana. PNAS. 2015;112:917–22.
Article
CAS
Google Scholar
Fehlmann T, Reinheimer S, Geng C, Su X, Drmanac S, Alexeev A, et al. cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs. Clin Epigenetics. 2016;8:123.
Article
Google Scholar