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Dimitrova AD, Georgiev O, Mishev K, Tzvetkov S, Ananiev ED, Karagyozov L. Mapping of unmethylated sites in rDNA repeats in barley NOR deletion line. JOURNAL OF PLANT PHYSIOLOGY 2016; 205:97-104. [PMID: 27649325 DOI: 10.1016/j.jplph.2016.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Extensive cytosine methylation is characteristic of plant rDNA. Evidence exists, however, that the active rRNA genes are less methylated. In this work we report on the mapping of unmethylated CCGG sites in Hordeum vulgare rDNA repeats by digestion with methylation sensitive restriction enzyme HpaII and indirect end-labeling of the generated fragments. For mapping we used genomic DNA from barley deletion line with a single NOR on chromosome 5H. This NOR is more active in order to compensate for the missing NOR 6H. The enhanced NOR 5H activity in the deletion mutant is not due to higher multiplicity of the rRNA genes or, as sequencing showed, to changes in the subunit structure of the intergenic spacer. The HpaII sites in barley rDNA are heavily methylated. Nevertheless, a fraction of the rDNA repeats is hypomethylated with unmethylated CCGG sites at various positions. One unmethylated CCGG sequence is close to the transcription start site, downstream of the 135bp subrepeats. Unmethylated sites are also present in the external transcribed spacer and in the genes coding mature rRNAs. The patterns of unmethylated sites in the barley deletion line and in lines with two NORs were compared. It is hypothesized that the occurrence of unmethylated sites on a fixed subset of rDNA repeats correlates with their transcriptional activity.
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Affiliation(s)
- Anna D Dimitrova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria.
| | - Oleg Georgiev
- Institute of Molecular Life Sciences, University Zurich-Irchel, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Kiril Mishev
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Stefan Tzvetkov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Evgueni D Ananiev
- Department of Plant Physiology, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
| | - Luchezar Karagyozov
- Department of Plant Physiology, Faculty of Biology, St. Kl. Ohridsky University of Sofia, 8 Dragan Tsankov bld., 1164 Sofia, Bulgaria
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Zhang W, Zhang T, Wu Y, Jiang J. Open Chromatin in Plant Genomes. Cytogenet Genome Res 2014; 143:18-27. [DOI: 10.1159/000362827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Lafon-Placette C, Faivre-Rampant P, Delaunay A, Street N, Brignolas F, Maury S. Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state. THE NEW PHYTOLOGIST 2013; 197:416-430. [PMID: 23253333 DOI: 10.1111/nph.12026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/02/2012] [Indexed: 05/17/2023]
Abstract
DNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relationships between gene-body DNA methylation, gene expression and chromatin compaction still need clarification. Here, DNA methylation was mapped in the noncondensed chromatin fraction from P. trichocarpa shoot apical meristematic cells, the center of plant morphogenesis, where DNA methylation variations could influence the developmental trajectory. DNase I was used to isolate the noncondensed chromatin fraction. Methylated sequences were immunoprecipitated, sequenced using Illumina/Solexa technology and mapped on the v2.0 poplar genome. Bisulfite sequencing of candidate sequences was used to confirm mapping data and to assess cytosine contexts and methylation levels. While the methylated DNase I hypersensitive site fraction covered 1.9% of the poplar genome, it contained sequences corresponding to 74% of poplar gene models, mostly exons. The level and cytosine context of gene-body DNA methylation varied with the structural characteristics of the genes. Taken together, our data show that DNA methylation is widespread and variable among genes in open chromatin of meristematic cells, in agreement with a role in their developmental trajectory.
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Affiliation(s)
- Clément Lafon-Placette
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, Orléans, 45067, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Orléans, 45067, France
| | - Patricia Faivre-Rampant
- INRA, UMR1165, UMR INRA / Université d'Evry, Unité de Recherche en Génomique Végétale, Centre de Recherche de Versailles-Grignon, Evry, 91057, France
| | - Alain Delaunay
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, Orléans, 45067, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Orléans, 45067, France
| | - Nathaniel Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, 901 87, Sweden
| | - Franck Brignolas
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, Orléans, 45067, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Orléans, 45067, France
| | - Stéphane Maury
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, Orléans, 45067, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Orléans, 45067, France
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