DNA Methylation and Demethylation in Arabidopsis

Gehring, Mary; Henikoff, Steven

doi:10.1199/tab.0102

Cited by 28 publications

(26 citation statements)

References 130 publications

(178 reference statements)

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“…In plants, there are separate sequence contexts subjected to demethylation (Gehring and Henikoff 2008) including the symmetric (CG, CHG), and asymmetric (CHH; where H is A, C, or T) ones (Gehring 2013). The demethylation controlled by the DNA glycosylase-lyases is performed via the excision of 5mC of fully or hemimethylated substrates with specificity towards CG, CHG or CHH sites.…”

Section: Dna Methylation Pattern Alterationsmentioning

confidence: 99%

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Plant tissue culture environment as a switch-key of (epi)genetic changes

Bednarek

Orłowska

2019

Plant Cell Tiss Organ Cult

102

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The in vitro tissue cultures are, beyond all difficulties, an essential tool in basic research as well as in commercial applications. Numerous works devoted to plant tissue cultures proved how important this part of the plant science is. Despite half a century of research on the issue of obtaining plants in in vitro cultures, many aspects remain unknown. The path associated with the reprogramming of explants in the fully functioning regenerants includes a series of processes that may result in the appearance of morphological, physiological, biochemical or, finally, genetic and epigenetic changes. All these changes occurring at the tissue culture stage and appearing in regenerants as tissue culture-induced variation and then inherited by generative progeny as somaclonal variation may be the result of oxidative stress, which works at the step of explant preparation, and in tissue culture as a result of nutrient components and environmental factors. In this review, we describe the current status of understanding the genetic and epigenetic changes that occur during tissue culture. Key message Variation appeared in regenerated plants as well as variation inherited by generative progeny of regenerants can may many, positive or negative impact, of gained plant materials. This review focused on factors that triggered this phenomenon with underlying oxidative stress.

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Section: Dna Methylation Pattern Alterationsmentioning

confidence: 99%

“…However, how 5-methylcytosine DNA glycosylases recognize their substrate is not apparent. One possibility is that they recognize the ends of genes (Gehring and Henikoff 2008).…”

Section: Dna Methylation Pattern Alterationsmentioning

confidence: 99%

Plant tissue culture environment as a switch-key of (epi)genetic changes

Bednarek

Orłowska

2019

Plant Cell Tiss Organ Cult

102

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“…CHG methylation is maintained by the chromomethylase CMT3, which also recognizes a modified histone, linking DNA methylation and histone methylation states (Law and Jacobsen, 2010). Perpetuation of asymmetric DNA methylation (CHH) requires an elaborate RNA-directed DNA methylation system (Law and Jacobsen, 2010;Gehring and Henikoff, 2008). Through mechanisms that are still not precisely biochemically or molecularly defined, de novo DNA methyltransferases are targeted to specific sequences by 24-nucleotide small RNAs to deposit CG and non-CG methylation at homologous sequences.…”

Section: Epigenetic Landscape In Vegetative Tissuesmentioning

confidence: 99%

“…The methylation patterns observed in the genome are the product of both DNA methyltransferase and DNA demethylase activity (Gehring and Henikoff, 2008). Arabidopsis contains four plantspecific DNA glycosylases that remove 5-methylcytosine from DNA: ROS1, DME, DML2, and DML3.…”

Section: Epigenetic Landscape In Vegetative Tissuesmentioning

confidence: 99%

Imprinted Gene Expression and the Contribution of Transposable Elements

Gehring

2013

Plant Transposons and Genome Dynamics in Evolution

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“…For example, most rice TEs show over 50% methylation (Kashkush and Khasdan 2007;Kishima et al 2007), while other genomic sequences show *16% methylation (Xiong et al 1999). In addition, the entire sequence of Arabidopsis TEs is usually methylated in all sequence contexts (Gehring and Henikoff 2008). However, Arabidopsis TEs can be reactivated in genetic backgrounds containing methylation-defective mutants (ddm1) or during tissue culture (Miura et al 2001;Singer et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains

Baruch

Kashkush

2011

Plant Cell Rep

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Transposable elements (TEs) dominate the genetic capacity of most eukaryotes, especially plants, where they may compose up to 90% of the genome. Many studies, both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes, and showed a high level of transpositional activity such as mPing family in rice. In this study, we have investigated in detail the copy number, insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family, termed TRIM, in nine rice strains, in comparison with mPing. While TRIM showed similar copy numbers (average of 79 insertions) in all the nine rice strains, the copy number of mPing varied dramatically (ranging from 6 to 203 insertions) in the same strains. Site-specific PCR analysis revealed that ~58% of the TRIM elements have identical insertion sites among the nine rice strains, while none of the mPing elements (100% polymorphism) have identical insertion sites in the same strains. Finally, over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains, while the level of the methylated mPing insertion sites ranged between 43 and 81.5%. The findings of this study indicate that unlike mPing, TRIM is most probably a fossil TE family in rice. In addition, the data shows that there might be a strong correlation between TE methylation and copy number.

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DNA Methylation and Demethylation in Arabidopsis

Cited by 28 publications

References 130 publications

Plant tissue culture environment as a switch-key of (epi)genetic changes

Plant tissue culture environment as a switch-key of (epi)genetic changes

Imprinted Gene Expression and the Contribution of Transposable Elements

Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains

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