Distribution of 5-methylcytosine residues in 5S rRNA genes in Arabidopsis thaliana and Secale cereale (original) (raw)
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Determining the conservation of DNA methylation in Arabidopsis
Epigenetics, 2009
A high-resolution map of DNA methylation in Arabidopsis has recently been generated using high-throughput sequencing of bisulfite-converted DNA. This detailed profile measures the methylation state of most of the cytosines in the Arabidopsis genome, and allows us for the first time to address questions regarding the conservation of methylation across duplicated regions of the genome. To address these questions we measured the degree to which methylation is conserved in both duplicated genes and duplicated non-coding regions of the genome. Methylation is controlled by different mechanisms and methyltransferases depending on the genomic location. Methylation in genes occurs primarily at CG sites and is controlled by the maintenance methyltransferase MET1. In contrast, an RNAi mediated methylation pathway that leads to de novo methylation of asymmetric CHH sites along with CG and CHG sites by the methyltransferase DRM2, drives methylation at tandem and inverted repeats. We find that the cytosine methylation profile is strongly preserved between duplicated genes and repeat regions. The highest level of conservation can be found at CG sites in genes and CHH sites in repeat regions. By constructing substitution matrices between aligned genes we see that methylated cytosines often pair with thymines, which may be explained by the spontaneous deamination of methyl-cytosine to thymine. Despite this observation, we find that methylated cytosines are less often paired with other nucleotides than non-methylated cytosines within gene bodies indicating that they may play an important functional role.
Plant Molecular Biology, 1991
The tomato nuclear genome was determined to have a G + C content of 37 ~o which is among the lowest reported for any plant species. Non-coding regions have a G + C content even lower (32~o average) whereas coding regions are considerably richer in G + C (46~o). 5-methyl cytosine was the only modified base detected and on average 23 ~o of the cytosine residues are methylated. Immature tissues and protoplasts have significantly lower levels of cytosine methylation (average 20 ~/o) than mature tissues (average 25 ~o )-Mature pollen has an intermediate level ofmethylation (22 ~/o). Seeds gave the highest value (27 ~o), suggesting de novo methylation after pollination and during seed development.
Journal of Global Innovations in Agriculture Sciences, 2021
Common DNA methylation controls gene expression and preserves genomic integrity. Mal methylation can cause developmental abnormalities in the plants. Multiple enzymes carrying out de novo methylation, methylation maintenance, and active demethylation culminate in a particular DNA methylation state. Next-generation sequencing advances and computational methods to analyze the data. The model plant Arabidopsis thaliana was used to study DNA methylation patterns, epigenetic inheritance, and plant methylation. Plant DNA methylation research reveals methylation patterns and describing variations in plant tissues. Determining the kinetics of DNA methylation in diverse plant tissues is also a new field. However, it is vital to understand regulatory and developmental decisions and use plant model species to develop new commercial crops; that are more resistant to stress and yield more. There are several methods available for assessing DNA methylation data. The performance of several techniqu...
Comparative analysis of DNA methylation in tobacco heterochromatic sequences
2000
Cytosine methylation levels and susceptibility to drug-induced hypomethylation have been studied in several Nicotiana tabacum (tobacco) DNA repetitive sequences. It has been shown using HapII, MspI, BamHI and Sau3AI methylation-sensitive restriction enzymes that the degree of 5 Hm C m CG-3 H methylation varied signi¢cantly between different repeats. There were almost saturation levels of 5-methylcytosine at the inner (3 H) cytosine position and variable degrees of methylation at the outer (5 H) cytosine at the enzyme recognition sites. The non-transcribed high copy satellite sequences (HRS60, GRS) displayed signi¢cant heterogeneity in methylation of their basic units while middle repetitive sequences (R8.1, GRD5, 5S rDNA) were more uniformly modi¢ed at both cytosine residues. Dihydroxypropyladenine (DHPA) treatment, which is thought to reduce DNA methyltransferase activity by increasing S-adenosylhomocysteine levels, resulted in extensive demethylation of the outer cytosine in all repeats, and the partial hypomethylation of cytosines at the inner positions in less densely methylated repeats such as HRS60 and GRS. The results suggest that hypomethylation of 5 Hm C m CG-3 H sites with DHPA is a gradual non-random process proceeding in the direction m C m CG 3 C m CG 3 CCG. The 18S-5.8S-25S rDNA was remarkably hypomethylated relative to the 5S rDNA at all restriction sites studied. Fluorescence in-situ hybridization showed that DNA decondensation within and between the 18S-5.8S-25S and 5S rDNA loci was variable in different nuclei. All nuclei had condensed and decondensed sequence. The chromatin of 18S-5.8S-25S rDNA was more readily digested with micrococcal nuclease than the 5S rDNA suggesting that the overall levels of decondensation were higher for 18S-5.8S-25S rDNA. Variable decondensation patterns within and between loci were also observed for GRS and HRS60. Cytosine methylation of the tobacco repeats is discussed with respect to transcription, overall levels of condensation and overall structure.
DNA methylation — an essential mechanism in plant molecular biology
Acta Physiologiae Plantarum, 2001
DNA methylation is a common phenomenon in plants. In plant genomes, its level is comparatively lower than that of animal genomes. It is involved in gene regulation and controls many development pathways. Methylation status of particular DNA sequence controls the potential for transition from vegetative to reproductive growth. It is believed that fully methylated elements are genetically and transcriptionally silent, however, some methylated genes may also be expressed. While hypomethylated elements are active and partially methylated elements, designated programmable, exhibit a variety of development expression programmes during plant development. DNA methylation plays an important role in the evolution of plant species through alloploidy or polyploidy. The methylation pattern in parental plants is highly heritable which is of great interest for plant breeders: DNA methylation also plays an important role in genome defense system by inactivating and methylating the invasive DNA sequences. A methylated sequence may suppress gene expression in other sequences. The generation and breeding of transgenic plants becomes complex due to inactivation of transgenes and instability of their expression. The pattern of methylation is maintained by methyltransferase through DNA replication. Several methods are in use to detect methylated nucleotides motifs that may help in identification of some essential genes.
5Methylcytosine content and methylation status in six millet DNAs
Journal of Biosciences, 1990
High performance liquid chromatographic analysis of the total nuclear DNAs of 6 millets plant species indicates that the 5-methylcytosine content ranges from 3% in barn yard millet to 9.6% in great millet while the fraction of cytosines methylated varies between 14% in little millet to 31 % in pearl millet. Digestion of millet DNAs with MspI/HpaII suggests that CpG methylation is more in great millet DNA while CpC methylation is more in the other 5 millet DNAs. Digestion of millet DNAs with MboI, Sau3AI andDpnI indicates that some of the5’ GATC3’ sequences are methylated at adenine and/or cytosine residues except in little millet where adenine methylation of the5’GATC3’ sequences is insignificant and there is a predominance of cytosine methylation in these sequences.
Recent Advances in DNA Methylation and Their Potential Breeding Applications in Plants
Horticulturae
Traditional plant breeding encompasses repetitive crossing and selection based on morphological traits, while phenotypic selection has been complemented by molecular methods in recent decades. Genome editing with techniques like the CRISPR-Cas9 system is still a novel approach that is being used to make direct modifications to nucleotide sequences of crops. In addition to these genetic alterations, an improved understanding of epigenetic variations such as DNA methylation on the phenotype of plants has led to increased opportunities to accelerate crop improvement. DNA methylation is the most widely studied epigenetic mark in plants and other eukaryotes. These epigenetic marks are highly conserved and involved in altering the activities and functions of developmental signals by catalyzing changes in the chromatin structure through methylation and demethylation. Cytosine methylation (5mC) is the most prevalent modification found in DNA. However, recent identification of N6-methyladeno...
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes
Current biology : CB, 2005
Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5' end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic,...
Large-scale methylation patterns in the nuclear genomes of plants
Gene, 1992
Methylation was investigated in compositional fractions of nuclear DNA preparations (50-100 kb in size) from five plants (onion, maize, rye, pea and tobacco), and was found to increase from GC-poor to GC-rich fractions. This methylation gradient showed different patterns in different plants and appears, therefore, to represent a novel, characteristic genome feature which concerns the noncoding, intergenic sequences that make up the bulk of the plant genomes investigated and mainly consist of repetitive sequences. The structural and functional implications of these results are discussed.
Non-symmetrical cytosine methylation in tobacco pollen DNA
Plant Molecular Biology, 1996
We have detected sequence-specific non-symmetrical cytosine methylation within a t40 bp region of the promoter for the tobacco auxin-binding protein gene T85 in pollen DNA. Direct sequencing of the population of bisulphite reaction products showed that, in this region, 10 out of a possible 49 cytosine residues were methylated at a high frequency in pollen whereas the corresponding region from somatic cells (leaf DNA) did not show a detectable level of methylation. The context of these sites was I x mSCpTpC, 1 x mSCpGpT, l x mSCpCpT, 2x mSCpTpT, 2x mSCpGpG, and 3x mSCpApT of which only mSCpGpG and mSCpGpT fitted the consensus sequence for symmetrical methylation in plants.