DNA methylation in higher plants: Past, present and future

Vanyushin, B. F.; Ashapkin, Vasily V.

doi:10.1016/j.bbagrm.2011.04.006

Cited by 181 publications

(127 citation statements)

References 73 publications

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“…A wide range of mechanisms that are genetic or supposedly epigenetic in origin have been recently described as possible causes of SV including TE (Transposable Element) transposition and small RNA directed DNA methylation (Smulders and de Klerk 2011;Neelakandan and Wang 2012). DNA methylation in the form of 5-Methylcytosine (5mC) is a major epigenetic mark involved in gene expression and plays an important role in plant regulation and development (Vanyushin and Ashapkin 2011). DNA methylation in plants commonly occurs at cytosine bases in all sequence contexts, the symmetric CG and CHG contexts (where H indicates A, T or C) and the asymmetric CHH contexts.…”

Section: Introductionmentioning

confidence: 99%

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Landey

Cenci²,

Guyot

et al. 2015

Plant Cell Tiss Organ Cult

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Long-term cell cultures were used in coffee to study the cytological, genetic and epigenetic changes occurring during cell culture ageing. The objective was to identify the mechanisms associated with somaclonal variation (SV). Three embryogenic cell lines were established in Coffea arabica (2n = 4x = 44) and somatic seedlings were regenerated after 4, 11 and 27 months. Phenotyping and AFLP, MSAP, SSAP molecular markers were performed on 199 and 124 plants, respectively. SV were only observed from the 11 and 27-month-old cultures, affecting 30 and 94 % of regenerated plants, respectively. Chromosome counts performed on 15 plants showed that normal plants systematically displayed normal chromosome numbers and that, conversely, aneuploidy (monosomy) was systematically found in variants. The allopolyploid structure of C. arabica allowed aneuploid cells to survive and regenerate viable plants. No polymorphic fragments were observed between the AFLP and SSAP electrophoretic profiles of mother plants and those of the in vitro progeny. Methylation polymorphism was low and ranged between 0.087 and 0.149 % irrespective of the culture age. The number of methylation changes per plant-normal or variant-was limited and ranged from 0 (55-80 % of the plants) to 4. The three cell lines showed similar SV rate increases during cell culture ageing and produced plants with similar molecular patterns indicating a non random process. The results showed that cell culture ageing is highly mutagenic in coffee and chromosomal rearrangements are directly linked to SV. Conversely, the analysis of methylation and transposable elements changes did not reveal any relation between the epigenetic patterns and SV.

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Section: Introductionmentioning

confidence: 99%

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Landey

Cenci²,

Guyot

et al. 2015

Plant Cell Tiss Organ Cult

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“…Combined with the four single-locus genes of organellar origin (all found in the EZ-MZ data set), a total of 17 organelle-related genes were found using the MSAP approach. Since organellar genomes are of bacterial origin, they exhibit mainly methylation of adenines and not of cytosines (Vanyushin and Ashapkin, 2011). Integration of organellar sequences in the nuclear genome is very common in many plant species, especially those that are outbreeding and have large genomes (Ayliffe et al, 1998).…”

Section: Differential Methylation Targets 59 and 39 Edges Of Genic Rementioning

confidence: 99%

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

et al. 2014

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DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 59 and 39 regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.DNA methylation is the covalent modification of nucleotides in DNA by the addition of a methyl group. In the nuclear genome of higher eukaryotes, 5-methylcytosine is the most important DNA modification (Goll and Bestor, 2005). It is a phenomenon of ancient origin predating plant-animal diversification. However, some differences exist between plant and animal methylome patterning and function, and DNA methylation has been found to be evolutionarily lost in a few species (Feng et al., 2010;Zemach et al., 2010). Eukaryotic DNA methylation is established by DNA methyltransferase (DMT) enzymes that transfer a methyl group from S-adenosyl Met to the fifth carbon of cytosine. These enzymes can largely be subdivided in maintenance and de novo DMTs, depending on whether the recognition site is already methylated or not. Maintenance DMTs conserve the methylation status of symmetrical (palindromic) sites after DNA replication, by recognizing the hemimethylated locus and methylating the newly synthesized strand. In plants, there are two types of maintenance DMTs: DNA METHYLTRANSFERASE (MET) and CHROMOMETHYLASE (CMT). The former methylates CG sites during DNA replication, whereas the latter methylates CHG (H = A, C, or T) sites located in chromatin in which histone 3 is dimethylated on Lys-9 (Goll and Bestor, 2005). De no...

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“…It was noted that the sequence of the diverged region of 'Kohi' was characteristic in terms of numbers of cytosine residues. Cytosine methylation in promoter regions is often found and the methylation levels influence downstream gene expressions (Vanyushin and Ashapkin, 2011). We thus suspected an epigenetic regulation for silencing Act1a.…”

Section: Resultsmentioning

confidence: 99%

Differential Constitution in Promoter Region Leads to a Phenotype with a Lower Allergic Actinidin Level in Yellow-fleshed Kiwifruit (<i>Actinidia chinensis</i>)

et al. 2018

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Actinidin is a major protein contained in kiwifruit (Actinidia spp.). While uptake of actinidin is beneficial to help gastric protein digestion with cysteine protease activity, the protein is also recognized as a major elicitor of allergy which can induce tingling in the oral cavity and occasionally severe anaphylactic reactions. Given that consumption of fresh kiwifruit has increased globally, development of Actinidia cultivars with lower level of actinidin is required to reduce the risk of allergenicity. In the present study, we examined variations in the actinidin level in Actinidia varieties. Among several varieties having trace amounts of actinidin, A. chinensis 'Kohi' was targeted to be analyzed for the molecular basis for the phenotype. 'Kohi' had below the detectable transcript level of Act1a, a critical gene for actinidin level. The upstream region of Act1a in 'Kohi' constituted different sequences from that of A. deliciosa 'Hayward', which has an active promoter for high expression of Act1a. The 'Kohi' sequence in the diverged region (upstream from −873 b) was rich in cytosine residues methylated at a higher level than in 'Hayward'. Our data suggest the possibility of novel epigenetic regulation to reduce the actinidin level. The molecular mechanism for the phenotype in 'Kohi' was differentiated from 'Hort16A', a globally popular cultivar with a low level of actinidin. This cultivar could be a choice as a genetic resource in breeding to develop cultivars with controlled actinidin levels.

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DNA methylation in higher plants: Past, present and future

Cited by 181 publications

References 73 publications

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

Differential Constitution in Promoter Region Leads to a Phenotype with a Lower Allergic Actinidin Level in Yellow-fleshed Kiwifruit (<i>Actinidia chinensis</i>)

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