Most cited article - PubMed ID 21274566
Inhibition of SAH-hydrolase activity during seed germination leads to deregulation of flowering genes and altered flower morphology in tobacco
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
In plants, genome duplication followed by genome diversification and selection is recognized as a major evolutionary process. Rapid epigenetic and genetic changes that affect the transcription of parental genes are frequently observed after polyploidization. The pattern of alternative splicing is also frequently altered, yet the related molecular processes remain largely unresolved. Here, we study the inheritance and expression of parental variants of three floral organ identity genes in allotetraploid tobacco. DEFICIENS and GLOBOSA are B-class genes, and AGAMOUS is a C-class gene. Parental variants of these genes were found to be maintained in the tobacco genome, and the respective mRNAs were present in flower buds in comparable amounts. However, among five tobacco cultivars, we identified two in which the majority of paternal GLOBOSA pre-mRNA transcripts undergo exon 3 skipping, producing an mRNA with a premature termination codon. At the DNA level, we identified a G-A transition at the very last position of exon 3 in both cultivars. Although alternative splicing resulted in a dramatic decrease in full-length paternal GLOBOSA mRNA, no phenotypic effect was observed. Our finding likely serves as an example of the initiation of homoeolog diversification in a relatively young polyploid genome.
- Keywords
- Alternative splicing, Floral genes, Flowering, Polyploidy, Tobacco,
- MeSH
- Alternative Splicing genetics MeSH
- Point Mutation genetics MeSH
- Exons genetics MeSH
- Transcription, Genetic * MeSH
- Homeodomain Proteins biosynthesis genetics MeSH
- Nucleotides genetics MeSH
- Polyploidy MeSH
- RNA Precursors genetics MeSH
- Gene Expression Regulation, Plant MeSH
- Plant Proteins biosynthesis genetics MeSH
- Nicotiana genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- GLOBOSA protein, plant MeSH Browser
- Homeodomain Proteins MeSH
- Nucleotides MeSH
- RNA Precursors MeSH
- Plant Proteins MeSH
Telomeres, nucleoprotein structures at the ends of linear eukaryotic chromosomes, are important for the maintenance of genomic stability. Telomeres were considered as typical heterochromatic regions, but in light of recent results, this view should be reconsidered. Asymmetrically located cytosines in plant telomeric DNA repeats may be substrates for a DNA methyltransferase enzyme and indeed, it was shown that these repeats are methylated. Here, we analyse the methylation of telomeric cytosines and the length of telomeres in Arabidopsis thaliana methylation mutants (met 1-3 and ddm 1-8), and in their wild-type siblings that were germinated in the presence of hypomethylation drugs. Our results show that cytosine methylation in telomeric repeats depends on the activity of MET1 and DDM1 enzymes. Significantly shortened telomeres occur in later generations of methylation mutants as well as in plants germinated in the presence of hypomethylation drugs, and this phenotype is stably transmitted to the next plant generation. A possible role of compromised in vivo telomerase action in the observed telomere shortening is hypothesized based on telomere analysis of hypomethylated telomerase knockout plants. Results are discussed in connection with previous data in this field obtained using different model systems.
- MeSH
- Arabidopsis enzymology genetics metabolism MeSH
- Cytosine metabolism MeSH
- Telomere Homeostasis MeSH
- DNA Methylation * MeSH
- Repetitive Sequences, Nucleic Acid MeSH
- Plants genetics metabolism MeSH
- Telomerase metabolism MeSH
- Telomere chemistry metabolism MeSH
- Telomere Shortening * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Cytosine MeSH
- Telomerase MeSH
BACKGROUND: DNA methylation plays a key role in development, contributes to genome stability, and may also respond to external factors supporting adaptation and evolution. To connect different types of stimuli with particular biological processes, identifying genome regions with altered 5-methylcytosine distribution at a genome-wide scale is important. Many researchers are using the simple, reliable, and relatively inexpensive Methylation Sensitive Amplified Polymorphism (MSAP) method that is particularly useful in studies of epigenetic variation. However, electrophoretic patterns produced by the method are rather difficult to interpret, particularly when MspI and HpaII isoschizomers are used because these enzymes are methylation-sensitive, and any C within the CCGG recognition motif can be methylated in plant DNA. RESULTS: Here, we evaluate MSAP patterns with respect to current knowledge of the enzyme activities and the level and distribution of 5-methylcytosine in plant and vertebrate genomes. We discuss potential caveats related to complex MSAP patterns and provide clues regarding how to interpret them. We further show that addition of combined HpaII + MspI digestion would assist in the interpretation of the most controversial MSAP pattern represented by the signal in the HpaII but not in the MspI profile. CONCLUSIONS: We recommend modification of the MSAP protocol that definitely discerns between putative hemimethylated mCCGG and internal CmCGG sites. We believe that our view and the simple improvement will assist in correct MSAP data interpretation.
- MeSH
- 5-Methylcytosine chemistry MeSH
- DNA, Plant genetics MeSH
- Epigenesis, Genetic MeSH
- DNA Methylation * MeSH
- Vertebrates genetics MeSH
- Polymorphism, Genetic * MeSH
- Restriction Mapping MeSH
- Nicotiana genetics MeSH
- Nucleic Acid Amplification Techniques methods MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- 5-Methylcytosine MeSH
- DNA, Plant MeSH
Telomere homeostasis is regulated at multiple levels, including the local chromatin structure of telomeres and subtelomeres. Recent reports demonstrated that a decrease in repressive chromatin marks, such as levels of cytosine methylation in subtelomeric regions, results in telomere elongation in mouse cells. Here we show that a considerable fraction of cytosines is methylated not only in subtelomeric, but also in telomeric DNA of tobacco BY-2 cells. Drug-induced hypomethylation (demonstrated at subtelomeric, telomeric, and global DNA levels) results in activation of telomerase. However, in contrast to mouse cells, the decrease in 5-methylcytosine levels and upregulation of telomerase do not result in any changes of telomere lengths. These results demonstrate the involvement of epigenetic mechanisms in the multilevel process of regulation of telomerase activity in plant cells and, at the same time, they indicate that changes in telomerase activity can be overridden by other factors governing telomere length stability.
- MeSH
- Adenine analogs & derivatives pharmacology MeSH
- Enzyme Activation drug effects MeSH
- Cytidine analogs & derivatives pharmacology MeSH
- DNA, Plant chemistry drug effects MeSH
- Epigenesis, Genetic MeSH
- Transcription, Genetic drug effects MeSH
- Cells, Cultured MeSH
- DNA Methylation drug effects MeSH
- Nucleosomes drug effects physiology MeSH
- Plant Proteins genetics metabolism MeSH
- Nicotiana cytology drug effects genetics metabolism MeSH
- Telomerase metabolism MeSH
- Telomere chemistry drug effects metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- 9-(2,3-dihydroxypropyl)adenine MeSH Browser
- Adenine MeSH
- Cytidine MeSH
- DNA, Plant MeSH
- Nucleosomes MeSH
- pyrimidin-2-one beta-ribofuranoside MeSH Browser
- Plant Proteins MeSH
- Telomerase MeSH
