Dna Methylation and Epigenetics

Bender, Judith

doi:10.1146/annurev.arplant.55.031903.141641

Cited by 318 publications

(225 citation statements)

References 136 publications

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“…When these modifications are lost or changed by specific mutations such as those in DDM1 or by continued passage in culture, both enhanced activation of transposons, and increased transcription of transposon-related elements is seen (Planckaert and Walbot, 1989;Kaeppler et al, 2000;. The mechanism for targeting particular regions of the genome for silencing via DNA and histone modifications is most likely mediated by RNA interference (Bender, 2004;Lippman and Martienssen, 2004). Interestingly, one of the DICERlike genes in Arabidopsis (DCL3, At3g43920) is upregulated 2.5-fold in habituated calli (Table IX).…”

Section: Discussionmentioning

confidence: 99%

“…These alterations in DNA methylation are maintained during the culture process, passed to plants regenerated from these callus cultures, and even passed to the progeny of plants regenerated from cultured cells (Kaeppler et al, 2000). Histone modifications, including methylation and acetylation of particular Lys residues, are also involved in chromatin structure and gene silencing (for review, see Loidl, 2003;Bender, 2004). In transcriptionally silent heterochromatin, for example, DNA methylation is often accompanied by Histone 3 methylation of Lys-9 (H3K9met), as well as Histone 4 hypoacetylation.…”

Section: Evidence For Epigenetic Modifications In Habituated Callus Cmentioning

confidence: 99%

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A Transcriptome-Based Characterization of Habituation in Plant Tissue Culture

Pischke¹,

Huttlin²,

Hegeman³

et al. 2006

Plant Physiology

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For the last 50 years, scientists have recognized that varying ratios of the plant hormones cytokinin and auxin induce plant cells to form particular tissues: undifferentiated calli, shoot structures, root structures, or a whole plant. Proliferation of undifferentiated callus tissue, greening, and the formation of shoot structures are all cytokinin-dependent processes. Habituation refers to a naturally occurring phenomenon whereby callus cultures, upon continued passage, lose their requirement for cytokinin. Earlier studies of calli with a higher-than-normal cytokinin content indicate that overproduction of cytokinin by the culture tissues is a possible explanation for this acquired cytokinin independence. A transcriptome-based analysis of a well established habituated Arabidopsis (Arabidopsis thaliana) cell culture line was undertaken, to explore genome-wide expression changes underlying the phenomenon of habituation. Increased levels of expression of the cytokinin receptor CRE1, as well as altered levels of expression of several other genes involved in cytokinin signaling, indicated that naturally acquired deregulation of cytokinin-signaling components could play a previously unrecognized role in habituation. Up-regulation of several cytokinin oxidases, downregulation of several known cytokinin-inducible genes, and a lack of regulation of the cytokinin synthases indicated that increases in hormone concentration may not be required for habituation. In addition, up-regulation of the homeodomain transcription factor FWA, transposon-related elements, and several DNA-and chromatin-modifying enzymes indicated that epigenetic changes contribute to the acquisition of cytokinin habituation.

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Section: Discussionmentioning

confidence: 99%

Section: Evidence For Epigenetic Modifications In Habituated Callus Cmentioning

confidence: 99%

A Transcriptome-Based Characterization of Habituation in Plant Tissue Culture

Pischke¹,

Huttlin²,

Hegeman³

et al. 2006

Plant Physiology

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“…For example, in plant systems that express double-stranded RNA (dsRNA) and "diced" small interfering RNAs (siRNAs) associated with RNA interference (RNAi), DNA sequences with identity to the aberrant RNAs can acquire cytosine methylation (Bender 2004). This RNA-directed DNA methylation (RdDM) is typically very specifically targeted, and results in dense CG and non-CG methylation.…”

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confidence: 99%

DNA Methylation of the Endogenous PAI Genes in Arabidopsis

Bender¹

2004

Cold Spring Harbor Symposia on Quantitative Biology

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In eukaryotes, the association of genomic DNA with histone proteins to form chromatin allows packaging of DNA into the nucleus. However, the degree of chromatin compaction varies along the length of each chromosome, with some regions present in relatively open transcriptionally active euchromatin, and some regions present in more compact transcriptionally silent heterochromatin. In particular, repetitive arrays associated with centromeres and ribosomal RNA-encoding genes (rDNA), as well as transposable element sequences (both DNA transposons and retrotransposons), are assembled into heterochromatin. In the case of repeat arrays, heterochromatin is likely to serve as a means of stabilizing these structures against rearrangement, whereas in the case of transposable elements heterochromatin serves as a means of genome defense against deleterious effects of their transcription and movement. Thus, the integrity of chromatin organization is critical for correct patterns of gene expression and genome stability. Key questions are how chromatin organization patterns are established, and how these patterns are maintained through cell divisions.In mammals and plants, as well as some species of fungi such as Neurospora crassa, heterochromatic regions of the genome are marked by cytosine methylation. Because this covalent DNA modification can be inherited as hemimethylated DNA after each round of replication, it provides an epigenetic memory of heterochromatin patterning in the previous generation. In mammals, cytosine methylation occurs almost exclusively in CG contexts, whereas in plants and Neurospora both CG and non-CG cytosines can be methylated. These differences reflect the different substrate specificities of DNA methyltransferase (DMTase) enzymes present in each organism.Heterochromatin is also associated with particular patterns of posttranslational modifications on the amino-terminal "tails" of histone proteins, which extend outward from the globular core of the histone octamer. For example, in many eukaryotes heterochromatin-associated modification patterns include methylation of histone H3 at lysine 9 (H3 mK9) and lack of acetylation (deacetylation) of lysines on H3 and H4. Conversely, euchromatin is associated with methylation of H3 at lysine 4 (H3 mK4) and hyperacetylation of lysines on H3 and H4. These and other posttranslational histone modifications are thought to constitute a "histone code" that guides the formation of heterochromatin, euchromatin, or specialized chromatin structures, most likely through recruitment of appropriate chromatin remodeling factors to histones carrying particular combinations of modifications (Jenuwein and Allis 2001).A striking recent discovery in Neurospora, Arabidopsis, and mammals is that cytosine methylation patterns can be guided by one of the heterochromatin-associated histone modifications, methylation of H3 at lysine 9. Neurospora presents the simplest example of this relationship: Loss of H3 mK9, either by mutation of the H3 K9 histone methyltransferase (HMTase) DIM-5 ...

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“…elements (TEs) are strictly regulated by epigenetic silencing mechanisms (Lisch 2009) and are major targets for DNA methylation in plant genomes (Bender 2004).…”

Section: Because Of Their Potentially Mutagenic Effects Transposablementioning

confidence: 99%

Assessing the Extent of Substitution Rate Variation of Retrotransposon Long Terminal Repeat Sequences in Oryza sativa and Oryza glaberrima

Zuccolo

Sebastian

et al. 2010

Rice

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Long Terminal Repeat retrotransposons (LTRRTs) are a major component of several plant genomes. Important insights into the evolutionary dynamics of these elements in a genome are provided by the comparative study of their insertion times. These can be inferred by the comparison of pairs of LTRs flanking intact LTR-RTs in combination with an estimated substitution rate. Over the past several years, different substitution rates have been proposed for LTRs in crop plants. However, very little is known about the extent of substitution rate variation and the factors contributing to this variation, so the rates currently used are generally considered rough estimators of actual rates. To evaluate the extent of substitution rate variation in LTRs, we identified 70 orthologous LTRs on the short arms of chromosome 3 of both Oryza sativa and Oryza glaberrima, species that diverged ∼0.64 Ma. Since these orthologous sequences were present in a common ancestor prior to species divergence, nucleotide differences identified in comparing these regions must correspond to mutations accumulated post-speciation, thereby giving us the opportunity to study LTR substitution rate variation in different elements across these short arms. As a control, we analyzed a similar amount of non-repeat-related sequences collected near the orthologous LTRs. Our analysis showed that substitution rate variation in LTRs is greater than 5-fold, is positively correlated with G+C content, and tends to increase near centromeric regions. We confirmed that in the vast majority of cases, LTRs mutate faster than their corresponding non-repeat-related neighboring sequences.

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Dna Methylation and Epigenetics

Cited by 318 publications

References 136 publications

A Transcriptome-Based Characterization of Habituation in Plant Tissue Culture

A Transcriptome-Based Characterization of Habituation in Plant Tissue Culture

DNA Methylation of the Endogenous PAI Genes in Arabidopsis

Assessing the Extent of Substitution Rate Variation of Retrotransposon Long Terminal Repeat Sequences in Oryza sativa and Oryza glaberrima

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