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Marenkova TV, Deineko EV. Hybridological analysis of inheritance of mosaic nptII gene expression in transgenic tobacco plants. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416060089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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K?í?ová K, Depicker A, Kova?ík A. Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture. Epigenetics 2013; 8:666-76. [PMID: 23770973 PMCID: PMC3857346 DOI: 10.4161/epi.24613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 11/19/2022] Open
Abstract
In plants, silencing is usually accompanied by DNA methylation and heterochromatic histone marks. We studied these epigenetic modifications in different epialleles of 35S promoter (P35S)-driven tobacco transgenes. In locus 1, the T-DNA was organized as an inverted repeat, and the residing neomycin phosphotransferase II reporter gene (P35S-nptII) was silenced at the posttranscriptional (PTGS) level. Transcriptionally silenced (TGS) epialleles were generated by trans-acting RNA signals in hybrids or in a callus culture. PTGS to TGS conversion in callus culture was accompanied by loss of the euchromatic H3K4me3 mark in the transcribed region of locus 1, but this change was not transmitted to the regenerated plants from these calli. In contrast, cytosine methylation that spread from the transcribed region into the promoter was maintained in regenerants. Also, the TGS epialleles generated by trans-acting siRNAs did not change their active histone modifications. Thus, both TGS and PTGS epialleles exhibit euchromatic (H3K4me3 and H3K9ac) histone modifications despite heavy DNA methylation in the promoter and transcribed region, respectively. However, in the TGS locus (271), abundant heterochromatic H3K9me2 marks and DNA methylation were present on P35S. Heterochromatic histone modifications are not automatically installed on transcriptionally silenced loci in tobacco, suggesting that repressive histone marks and cytosine methylation may be uncoupled. However, transient loss of euchromatic modifications may guide de novo DNA methylation leading to formation of stable repressed epialleles with recovered eukaryotic marks. Compilation of available data on epigenetic modification of inactivated P35S in different systems is provided.
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Affiliation(s)
- Kate?ina K?í?ová
- Institute of Biophysics, Academy of Sciences; Královopolská, Brno, Czech Republic
| | - Ann Depicker
- Department of Plant Systems Biology; VIB; Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Gent, Belgium
| | - Ale? Kova?ík
- Institute of Biophysics, Academy of Sciences; Královopolská, Brno, Czech Republic
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3
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Vermeersch L, De Winne N, Nolf J, Bleys A, Kovařík A, Depicker A. Transitive RNA silencing signals induce cytosine methylation of a transgenic but not an endogenous target. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:867-879. [PMID: 23480471 DOI: 10.1111/tpj.12172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/25/2013] [Accepted: 03/04/2013] [Indexed: 05/27/2023]
Abstract
Post-transcriptional gene silencing of a primary target gene in plants can coincide with the production of secondary small interfering RNAs (siRNAs) of coding sequences adjacent to the target region and with de novo RNA-directed DNA methylation (RdDM) thereof. Here, we analyzed the susceptibility of transgenic and endogenous targets to RdDM induced by primary and secondary silencing signals. In three different configurations, primary silencing signals were able to direct in trans methylation of chimeric transgenes and the CATALASE2 (CAT2) endogene; however, extensive spreading of methylation occurred only in the transgene, resulting in the methylation of the flanking CAT2 sequence, whereas methylation of the CAT2 endogene was restricted to the target region and the enclosed introns. The secondary silencing signals arising from this transgenic primary target simultaneously silenced a secondary transgene target and the CAT2 endogene, but were only capable of directing RdDM to the transgene. Our data indicate that RdDM is correlated with the in situ generation of secondary siRNAs, occurring in P35S-driven transgenes but not in most endogenes. We conclude that although both endogenes and transgenes are equally sensitive to transitive silencing, differences exist in their susceptibility to undergo secondary RdDM.
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Affiliation(s)
- Leen Vermeersch
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
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Kasai M, Koseki M, Goto K, Masuta C, Ishii S, Hellens RP, Taneda A, Kanazawa A. Coincident sequence-specific RNA degradation of linked transgenes in the plant genome. PLANT MOLECULAR BIOLOGY 2012; 78:259-73. [PMID: 22146813 DOI: 10.1007/s11103-011-9863-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/18/2011] [Indexed: 05/23/2023]
Abstract
The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype. Although neomycin phosphotransferase II (nptII), a marker gene co-introduced into the genome with the CHS-A transgene, is not normally silenced in petunia, even when CHS-A is silenced, here we found that nptII was silenced in a petunia line in which CHS-A PTGS was induced, but not in the revertant plants that had no PTGS of CHS-A. Transcriptional activity, accumulation of short interfering RNAs, and restoration of mRNA level after infection with viruses that had suppressor proteins of gene silencing indicated that the mechanism for nptII silencing was posttranscriptional. Read-through transcripts of the CHS-A gene toward the nptII gene were detected. Deep-sequencing analysis revealed a striking difference between the predominant size class of small RNAs produced from the read-through transcripts (22 nt) and that from the CHS-A RNAs (21 nt). These results implicate the involvement of read-through transcription and distinct phases of RNA degradation in the coincident PTGS of linked transgenes and provide new insights into the destabilization of transgene expression.
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Affiliation(s)
- Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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5
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Crhák Khaitová L, Fojtová M, Křížová K, Lunerová J, Fulneček J, Depicker A, Kovařík A. Paramutation of tobacco transgenes by small RNA-mediated transcriptional gene silencing. Epigenetics 2011; 6:650-60. [PMID: 21521939 PMCID: PMC3121974 DOI: 10.4161/epi.6.5.15764] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 04/06/2011] [Indexed: 02/03/2023] Open
Abstract
It has been well established that trans-acting small RNAs guide promoter methylation leading to its inactivation and gene silencing at the transcriptional level (TGS). Here we addressed the question of the influence of the locus structure and epigenetic modifications of the target locus on its susceptibility for being paramutated by trans-acting small RNA molecules. Silencing was induced by crossing a 35S promoter silencer locus 271 with two different 35S-driven transgene loci, locus 2 containing a highly expressed single copy gene and locus 1 containing an inverted posttranscriptionally silenced (PTGS) repeat of this gene. Three generations of exposure to RNA signals from the 271 locus were required to complete silencing and methylation of the 35S promoter within locus 2. Segregating methylated locus 2 epialleles were obtained only from the third generation of hybrids, and this methylation was not correlated with silencing. Strikingly, only one generation was required for the PTGS locus 1 to acquire complete TGS and 35S promoter methylation. In this case, paramutated locus 1 epialleles bearing methylated and inactive 35S promoters segregated already from the first generation of hybrids. The results support the hypothesis that PTGS loci containing a palindrome structure and methylation in the coding region are more sensitive to paramutation by small RNAs and exhibit a strong tendency to formation of meiotically transmissible TGS epialleles. These features contrast with a non-methylated single copy transgenic locus that required several generations of contact with RNA silencing molecules to become imprinted in a stable epiallele.
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Affiliation(s)
- Lucie Crhák Khaitová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
| | - Miloslava Fojtová
- Department of Functional Genomics and Proteomics; Institute of Experimental Biology; Faculty of Science; Masaryk University; Brno, Czech Republic
| | - Kateřina Křížová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
| | - Jana Lunerová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
| | - Jaroslav Fulneček
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
| | - Anna Depicker
- Department of Plant Systems Biology; VIB; Department of Plant Biotechnology and Genetics; Ghent University; Ghent, Belgium
| | - Aleš Kovařík
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
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6
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Krizova K, Fojtova M, Depicker A, Kovarik A. Cell culture-induced gradual and frequent epigenetic reprogramming of invertedly repeated tobacco transgene epialleles. PLANT PHYSIOLOGY 2009; 149:1493-504. [PMID: 19129419 PMCID: PMC2649402 DOI: 10.1104/pp.108.133165] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 12/22/2008] [Indexed: 05/04/2023]
Abstract
Using a two-component transgene system involving two epiallelic variants of the invertedly repeated transgenes in locus 1 (Lo1) and a homologous single-copy transgene locus 2 (Lo2), we have studied the stability of the methylation patterns and trans-silencing interactions in cell culture and regenerated tobacco (Nicotiana tabacum) plants. The posttranscriptionally silenced (PTGS) epiallele of the Lo1 trans-silences and trans-methylates the target Lo2 in a hybrid (Lo1/Lo2 line), while its transcriptionally silenced variant (Lo1E) does not. This pattern was stable over several generations in plants. However, in early Lo1E/Lo2 callus, decreased transgene expression and partial loss of Lo1E promoter methylation compared with leaf tissue in the parental plant were observed. Analysis of small RNA species and coding region methylation suggested that the transgenes were silenced by a PTGS mechanism. The Lo1/Lo2 line remained silenced, but the nonmethylated Lo1 promoter acquired partial methylation in later callus stages. These data indicate that a cell culture process has brought both epialleles to a similar epigenetic ground. Bisulfite sequencing of the 35S promoter within the Lo1 silencer revealed molecules with no, intermediate, and high levels of methylation, demonstrating, to our knowledge for the first time, cell-to-cell methylation diversity of callus. Regenerated plants showed high interindividual but low intraindividual epigenetic variability, indicating that the callus-induced epiallelic variants were transmitted to plants and became fixed. We propose that epigenetic changes associated with dedifferentiation might influence regulatory pathways mediated by trans-PTGS processes.
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Affiliation(s)
- Katerina Krizova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
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7
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Lunerová-Bedrichová J, Bleys A, Fojtová M, Khaitová L, Depicker A, Kovarík A. Trans-generation inheritance of methylation patterns in a tobacco transgene following a post-transcriptional silencing event. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:1049-62. [PMID: 18315537 DOI: 10.1111/j.1365-313x.2008.03475.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We have studied the inheritance of the epigenetic state of tobacco transgenes whose expression was post-transcriptionally silenced by an invertedly repeated silencer locus. We show that, in hybrids, the coding region of the target neomycin phosphotransferase (nptII) gene was almost exclusively methylated at CG configurations, and dense non-CG methylation occurred in the 3' untranslated region. Homologous sequences in the silencer locus were heavily methylated at both CG and non-CG motifs. After segregation of the silencer locus, the CG methylation but not the non-CG methylation of the target genes was transmitted to the progeny. In the segregants, we observed an overall increase of CG methylation in the target genes, associated with a re-distribution from the 3' end of the coding region towards the middle. This pattern was inherited with some fluctuation for at least two additional generations in the absence of a detectable T-DNA-derived small RNA fraction. Thus CG methylation is not cleared during meiosis and may be inherited over generations without RNA signals being present. These epi-allelic variants re-expressed the reporter gene immediately after segregation of the trigger, showing that relatively dense CG methylation (approximately 60-80%) imprinted on most of the coding region (>500 bp) did not reduce expression compared with the parental non-methylated locus. We propose that the genic CG methylation seen in euchromatic regions of the genome may originate from ancient post-transcriptional gene silencing events as a result of adventitiously produced methylation-directing RNA molecules.
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Affiliation(s)
- Jana Lunerová-Bedrichová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., CZ-61265 Brno, Czech Republic
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8
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Marjanac G, De Paepe A, Peck I, Jacobs A, De Buck S, Depicker A. Evaluation of CRE-mediated excision approaches in Arabidopsis thaliana. Transgenic Res 2007; 17:239-50. [PMID: 17541719 DOI: 10.1007/s11248-007-9096-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 03/26/2007] [Indexed: 10/23/2022]
Abstract
The ability of the CRE recombinase to catalyze excision of a DNA fragment flanked by directly repeated lox sites has been exploited to modify gene expression and proved to function well in particular case studies. However, very often variability in CRE expression and differences in efficiency of CRE-mediated recombination are observed. Here, various approaches were investigated to reproducibly obtain optimal CRE activity. CRE recombination was analyzed either by transforming the CRE T-DNA into plants containing a lox-flanked fragment or by transforming a T-DNA harboring a lox-flanked fragment into plants producing the CRE recombinase. Although somatic CRE-mediated excision of a lox-flanked fragment was obtained in all transformants, a variable amount of germline-transmitted deletions was found among different independent transformants, irrespective of the orientation of transformation. Also, the efficiency of CRE-mediated excision correlated well with the CRE mRNA level. In addition, CRE-mediated fragment excision was compared after floral dip and after root tissue transformation when transforming in a CRE-expressing background. Importantly, less CRE activity was needed to excise the lox-flanked fragment from the transferred T-DNA after root tissue transformation than after floral dip transformation. We hypothesize that this is correlated with the lower T-DNA copy number inserted during root transformation as compared to floral dip transformation.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/growth & development
- DNA, Bacterial/genetics
- DNA, Plant/genetics
- Gene Expression Regulation, Plant
- Genome, Plant
- Glucuronidase/metabolism
- Integrases/genetics
- Integrases/metabolism
- Plant Roots/genetics
- Plant Roots/growth & development
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/growth & development
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombination, Genetic
- Reverse Transcriptase Polymerase Chain Reaction
- Transformation, Genetic
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Affiliation(s)
- Gordana Marjanac
- Department of Plant Systems Biology, VIB, Technologiepark 927, Gent 9052, Belgium
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9
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Fojtová M, Bleys A, Bedřichová J, Van Houdt H, Křížová K, Depicker A, Kovařík A. The trans-silencing capacity of invertedly repeated transgenes depends on their epigenetic state in tobacco. Nucleic Acids Res 2006; 34:2280-93. [PMID: 16670434 PMCID: PMC1456325 DOI: 10.1093/nar/gkl180] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 03/13/2006] [Accepted: 03/22/2006] [Indexed: 11/13/2022] Open
Abstract
We studied the in trans-silencing capacities of a transgene locus that carried the neomycin phosphotransferase II reporter gene linked to the 35S promoter in an inverted repeat (IR). This transgene locus was originally posttranscriptionally silenced but switched to a transcriptionally silenced epiallele after in vitro tissue culture. Here, we show that both epialleles were strongly methylated in the coding region and IR center. However, by genomic sequencing, we found that the 1.0 kb region around the transcription start site was heavily methylated in symmetrical and non-symmetrical contexts in transcriptionally but not in posttranscriptionally silenced epilallele. Also, the posttranscriptionally silenced epiallele could trans-silence and trans-methylate homologous transgene loci irrespective of their genomic organization. We demonstrate that this in trans-silencing was accompanied by the production of small RNA molecules. On the other hand, the transcriptionally silenced variant could neither trans-silence nor trans-methylate homologous sequences, even after being in the same genetic background for generations and meiotic cycles. Interestingly, 5-aza-2-deoxy-cytidine-induced hypomethylation could partially restore signaling from the transcriptionally silenced epiallele. These results are consistent with the hypothesis that non-transcribed highly methylated IRs are poor silencers of homologous loci at non-allelic positions even across two generations and that transcription of the inverted sequences is essential for their trans-silencing potential.
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Affiliation(s)
- Miloslava Fojtová
- Institute of Biophysics, Academy of Sciences of the Czech RepublicCZ-612 65 Brno, Czech Republic
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Annick Bleys
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Jana Bedřichová
- Institute of Biophysics, Academy of Sciences of the Czech RepublicCZ-612 65 Brno, Czech Republic
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Helena Van Houdt
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Kateřina Křížová
- Institute of Biophysics, Academy of Sciences of the Czech RepublicCZ-612 65 Brno, Czech Republic
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Anna Depicker
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Aleš Kovařík
- To whom correspondence should be addressed at Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ 612 65 Brno, Czech Republic. Tel: +420 541 517 178; Fax: +420 541 211 293;
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Koukalova B, Fojtova M, Lim KY, Fulnecek J, Leitch AR, Kovarik A. Dedifferentiation of tobacco cells is associated with ribosomal RNA gene hypomethylation, increased transcription, and chromatin alterations. PLANT PHYSIOLOGY 2005; 139:275-86. [PMID: 16113227 PMCID: PMC1203377 DOI: 10.1104/pp.105.061788] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 05/31/2005] [Accepted: 05/31/2005] [Indexed: 05/04/2023]
Abstract
Epigenetic changes accompanying plant cell dedifferentiation and differentiation are reported in 35S ribosomal DNA (rDNA) of tobacco (Nicotiana tabacum). There was a reduction of CG and CNG methylation in both intergenic and genic regions of the rDNA cistron in fully dedifferentiated callus and root compared to leaf. The rDNA hypomethylation was not random, but targeted to particular rDNA gene families at units that are clustered within the tandem array. The process of hypomethylation was initiated as early as 2 weeks after the callus induction and established epigenetic patterns were stably maintained throughout prolonged culture. However, regenerated plants and their progeny showed partial and complete remethylation of units, respectively. Nuclear run-on assays revealed a 2-fold increase of primary (unprocessed) ribosomal RNA transcripts in callus compared to leaf tissue. However, the abundance of mature transcripts in callus was elevated by only about 25%. Fluorescence in situ hybridization analysis of interphase nuclei showed high levels of rDNA chromatin condensation in both callus and leaf, with substantially less decondensed rDNA than is observed in meristematic root-tip cells. It is likely that the regions of the rDNA locus showing decondensation correspond to the clusters of hypomethylated units that occur in the tandem array at each locus. The data together indicate that the establishment of pluripotency and cell proliferation occurring with callus induction is associated with enhanced ribosomal RNA gene expression and overall rDNA hypomethylation, but is not associated with material-enhanced relaxation of chromatin structure (decondensation) at rDNA loci.
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Affiliation(s)
- Blazena Koukalova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno
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García-Pérez RD, Houdt HV, Depicker A. Spreading of post-transcriptional gene silencing along the target gene promotes systemic silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 38:594-602. [PMID: 15125766 DOI: 10.1111/j.1365-313x.2004.02067.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Transitive silencing and grafting-induced gene silencing phenomena were combined to investigate whether a primary target beta-glucuronidase (gus) gene could promote the generation of systemic transitive silencing signals. Tobacco plants with hemizygous or homozygous silencer locus and in trans silenced primary target were used as a source of post-transcriptionally silenced rootstocks and tobacco plants with or without a secondary target locus as scion source. The silencer locus harbored two identical neomycin phosphotransferase II (nptII)-containing T-DNAs, integrated as an inverted repeat. The primary target locus carried a gus gene with homology to the transcribed region of the nptII gene only in the 3' untranslated region, whereas the secondary target locus had two or more copies of a gus gene without homology to transcribed sequences of the silencer locus. The upstream region of the initially targeted sequences of the in trans silenced gus gene could induce the production of a systemic signal. This signal was capable of triggering post-transcriptional gene silencing (PTGS) of the secondary target gus genes in the scion. In addition, the induction of systemic silencing was strikingly dosage dependent for the silencer as well as the primary target loci in the rootstock. Moreover, in the scions, the secondary target gus genes had to be present to generate detectable amounts of short interfering RNAs.
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Affiliation(s)
- Rubén Darío García-Pérez
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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12
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Fojtova M, Van Houdt H, Depicker A, Kovarik A. Epigenetic switch from posttranscriptional to transcriptional silencing is correlated with promoter hypermethylation. PLANT PHYSIOLOGY 2003; 133:1240-50. [PMID: 14551338 PMCID: PMC281619 DOI: 10.1104/pp.103.023796] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2003] [Revised: 05/14/2003] [Accepted: 07/01/2003] [Indexed: 05/19/2023]
Abstract
Changes in the distribution of methylcytosine residues along a transgene locus of tobacco (Nicotiana tabacum) in relation to the type of gene silencing were studied in parental plant leaves, calli, and regenerated plants derived thereof. Parental-silenced HeLo1 (hemizygous for locus 1) plants show posttranscriptional silencing of the residing nptII (neomycin phosphotransferase II) transgene and cytosine methylation restricted to the 3' end and center part of the transcribed region. Here, we report that with an increasing number of cell cycles, DNA methylation changes gradually, and methylation is introduced into the promoter during cell culture and more slowly in vegetatively propagated plants. After 24 months of callus in vitro cultivation, an epigenetic variant, designated locus 1E, was obtained in which cytosine methylation of symmetrical (CG and CNG) sites was almost complete within the 5' end of the nptII-transcribed region and the 35S promoter. Further, methylation of nonsymmetrical sites appeared de novo in the promoter, whereas this type of methylation was significantly reduced in the 3' end of the transcribed region when compared with locus 1. The newly established epigenetic patterns were stably transmitted from calli into regenerated plants and their progeny. The protein and steady-state RNA levels remained low in locus 1E, whereas with nuclear run-on assays, no detectable amounts of primary transcripts were found along the nptII gene, indicating that the methylated promoter became inactivated. The results suggest that a switch between posttranscriptional and transcriptional gene silencing could be a mechanism leading to irrevocable shut down of gene expression within a finite number of generations.
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Affiliation(s)
- Miloslava Fojtova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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13
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Lechtenberg B, Schubert D, Forsbach A, Gils M, Schmidt R. Neither inverted repeat T-DNA configurations nor arrangements of tandemly repeated transgenes are sufficient to trigger transgene silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 34:507-517. [PMID: 12753589 DOI: 10.1046/j.1365-313x.2003.01746.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Transgene expression was analysed in Arabidopsis T-DNA transformants carrying defined numbers and arrangement of different reporter genes. All transgenes were placed under the control of the strong constitutive CaMV 35S promoter. High, stable transgene expression was observed in plants containing two copies of the beta-glucuronidase (GUS) gene, two or four copies of the green fluorescent protein (GFP) gene and two, four or six copies of the streptomycin phosphotransferase (SPT) gene. Thus, the mere presence of multiple promoter and/or transgene sequences did not result in gene silencing. In none of the cases analysed were tandem repeat arrangements of transgenes and/or inverted repeat (IR) T-DNA structures sufficient to trigger silencing of the different reporter genes. Instead, post-transcriptional gene silencing (PTGS) correlated with the copy number of the highly expressed transgenes. Twelve copies of the SPT and four copies of the GUS gene triggered silencing. Silencing is frequently associated with repetitive T-DNA structures. We favour the idea that in many cases this may be attributed to the high transgene doses rather than the repeat arrangements themselves.
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Affiliation(s)
- Berthold Lechtenberg
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
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14
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Van Houdt H, Bleys A, Depicker A. RNA target sequences promote spreading of RNA silencing. PLANT PHYSIOLOGY 2003; 131:245-53. [PMID: 12529532 PMCID: PMC166804 DOI: 10.1104/pp.009407] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2002] [Revised: 08/03/2002] [Accepted: 10/02/2002] [Indexed: 05/18/2023]
Abstract
It is generally recognized that a silencing-inducing locus can efficiently reduce the expression of genes that give rise to transcripts partially homologous to those produced by the silencing-inducing locus (primary targets). Interestingly, the expression of genes that produce transcripts without homology to the silencing-inducing locus (secondary targets) can also be decreased dramatically via transitive RNA silencing. This phenomenon requires primary target RNAs that contain sequences homologous to secondary target RNAs. Sequences upstream from the region homologous to the silencing inducer in the primary target transcripts give rise to approximately 22-nucleotide small RNAs, coinciding with the region homologous to the secondary target. The presence of these small RNAs corresponds with reduced expression of the secondary target whose transcripts are not homologous to the silencing inducer. The data suggest that in transgenic plants, targets of RNA silencing are involved in the expansion of the pool of functional small interfering RNAs. Furthermore, methylation of target genes in sequences without homology to the initial silencing inducer indicates not only that RNA silencing can expand across target RNAs but also that methylation can spread along target genes.
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Affiliation(s)
- Helena Van Houdt
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Karel Lodewijk Ledeganckstraat 35, B-9000 Ghent, Belgium
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Abstract
In plants, double-stranded RNA can silence genes by triggering degradation of homologous RNA in the cytoplasm and by directing methylation of homologous nuclear DNA sequences. Analyses of Arabidopsis mutants and plant viral suppressors of silencing are unraveling RNA-silencing mechanisms, which require common proteins in diverse organisms, and are assessing the role of methylation in transcriptional and posttranscriptional gene silencing.
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Affiliation(s)
- M A Matzke
- Institute of Molecular Biology, Austrian Academy of Sciences, Billrothstrasse 11, A-5020, Salzburg, Austria.
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16
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Kovarík A, Van Houdt H, Holý A, Depicker A. Drug-induced hypomethylation of a posttranscriptionally silenced transgene locus of tobacco leads to partial release of silencing. FEBS Lett 2000; 467:47-51. [PMID: 10664454 DOI: 10.1016/s0014-5793(00)01077-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effect of DNA methylation upon posttranscriptional gene silencing (PTGS) has been investigated in transgenic tobacco lines showing PTGS and methylation of the neomycin phosphotransferase II (nptII) reporter genes. Application of the hypomethylation drugs dihydroxypropyladenine or 5-azacytidine resulted in approximately 30% reduced methylation of cytosines located in a non-symmetrical context in the 3' untranslated region of the nptII transgenes. The hypomethylation was accompanied by up to 12-fold increase in NPTII protein levels, suggesting that methylation of non-symmetrical motifs may account for an increased degree of PTGS. Models for the possible role of DNA methylation in PTGS are discussed.
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Affiliation(s)
- A Kovarík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic.
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