Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine

Baubec, Tuncay; Pečinka, Aleš; Rozhon, Wilfried; Scheid, Ortrun Mittelsten

doi:10.1111/j.1365-313x.2008.03699.x

Cited by 115 publications

(160 citation statements)

References 60 publications

Supporting

Mentioning

152

Contrasting

Order By: Relevance

“…Zebularine can trigger the reactivation of transcriptionally silenced genes with a ∼15-25% local reduction in DNA methylation levels (60). Bisulfite analysis of cotyledon DNA confirmed a similar decrease in DNA methylation levels in all sequence contexts at the LTR AtGP1 locus upon incubation with zebularine in both dark-and light conditions (Fig.…”

Section: Heterochromatin Rearrangements and Attenuation Of Tgs Arementioning

confidence: 62%

Light signaling controls nuclear architecture reorganization during seedling establishment

Bourbousse

Mestiri

Zabulon

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

108

View full text Add to dashboard Cite

The spatial organization of chromatin can be subject to extensive remodeling in plant somatic cells in response to developmental and environmental signals. However, the mechanisms controlling these dynamic changes and their functional impact on nuclear activity are poorly understood. Here, we determined that light perception triggers a switch between two different nuclear architectural schemes during Arabidopsis postembryonic development. Whereas progressive nucleus expansion and heterochromatin rearrangements in cotyledon cells are achieved similarly under light and dark conditions during germination, the later steps that lead to mature nuclear phenotypes are intimately associated with the photomorphogenic transition in an organ-specific manner. The light signaling integrators DE-ETIOLATED 1 and CONSTITUTIVE PHOTOMORPHOGENIC 1 maintain heterochromatin in a decondensed state in etiolated cotyledons. In contrast, under light conditions cryptochrome-mediated photoperception releases nuclear expansion and heterochromatin compaction within conspicuous chromocenters. For all tested loci, chromatin condensation during photomorphogenesis does not detectably rely on DNA methylation-based processes. Notwithstanding, the efficiency of transcriptional gene silencing may be impacted during the transition, as based on the reactivation of transposable element-driven reporter genes. Finally, we report that global engagement of RNA polymerase II in transcription is highly increased under light conditions, suggesting that cotyledon photomorphogenesis involves a transition from globally quiescent to more active transcriptional states. Given these findings, we propose that light-triggered changes in nuclear architecture underlie interplays between heterochromatin reorganization and transcriptional reprogramming associated with the establishment of photosynthesis. plant development | photomorphogenesis | light signaling | nuclear organization | heterochromatin C hromatin allows dense packaging of chromosomal DNA into a small and constrained nuclear space. It also serves as a structural framework for regulatory processes that control the functional status of genome domains with variable sizes, notably by dynamically influencing the subnuclear partitioning of generich and repeat-rich domains within euchromatic and heterochromatic regions, respectively (reviewed in refs. 1-3). These chromatin-based processes impact plasticity in the regulation of nuclear programs during both vegetative and reproductive phases of the plant life cycle (recently reviewed in refs. 4-8). In many cases, such events combine local chromatin variations with prominent changes in nuclear architecture and higher-order chromatin organization.Spatial chromatin organization is well exemplified by the extreme cases of transcriptionally silent chromocenters that contain the majority of ribosomal DNA repeats, such as the (peri)centromeric domains of mice and several plant species that include transposable elements (TE) and non-TE repeated sequences (9,

show abstract

Section: Heterochromatin Rearrangements and Attenuation Of Tgs Arementioning

confidence: 62%

Light signaling controls nuclear architecture reorganization during seedling establishment

Bourbousse

Mestiri

Zabulon

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

108

View full text Add to dashboard Cite

show abstract

“…S5) but DNA methylation is very low in flies 34 , we hypothesized that cytosine methylation contributes to low DNA accessibility in Arabidopsis. This hypothesis was tested by treating seedlings with 5-azacytidine, which is an established method to deplete the Arabidopsis genome of cytosine methylation [35][36][37] . In treated seedlings, accessibility of tested long genes and TE genes increased strongly and became similar to that of accessible active genes (Fig.…”

Section: Resultsmentioning

confidence: 99%

Distinct modes of DNA accessibility in plant chromatin

et al. 2012

View full text Add to dashboard Cite

The accessibility of DNA to regulatory proteins is a major property of the chromatin environment that favours or hinders transcription. Recent studies in flies reported that H3K9me2-marked heterochromatin is accessible while H3K27me3-marked chromatin forms extensive domains of low accessibility. Here we show that plants regulate DNA accessibility differently. H3K9me2-marked heterochromatin is the least accessible in the Arabidopsis thaliana genome, and H3K27me3-marked chromatin also has low accessibility. We see that very long genes without H3K9me2 or H3K27me3 are often inaccessible and generated significantly lower amounts of antisense transcripts than other genes, suggesting that reduced accessibility is associated with reduced recognition of alternative promoters. Low accessibility of H3K9me2-marked heterochromatin and long genes depend on cytosine methylation, explaining why chromatin accessibility differs between plants and flies. Together, we conclude that restriction of DNA accessibility is a local property of chromatin and not necessarily a consequence of microscopically visible compaction.

show abstract

“…In this model species, seed exposure to either 5-azacytidine (5azaC) or zebularine imposes a dose-dependent loss of DNA methylation at the seedling stage, which, at higher concentrations (>50 µM), was larger for 5azaC [20]. Interestingly, demethylation induced by the two compounds occurred in all sequence contexts and altered both gene and TE expression [19,20].…”

Section: Introductionmentioning

confidence: 96%

“…Zebularine is chemically more stable, forms a reversible complex with DNMTs, and exhibits a weaker inhibition activity and cytotoxicity than azacytosine analogs [13]. A comprehensive analysis of the molecular response to treatment with these DNMTi in plants is only available for the model Arabidopsis thaliana [19,20]. In this model species, seed exposure to either 5-azacytidine (5azaC) or zebularine imposes a dose-dependent loss of DNA methylation at the seedling stage, which, at higher concentrations (>50 µM), was larger for 5azaC [20].…”

Section: Introductionmentioning

confidence: 99%

Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

et al. 2017

View full text Add to dashboard Cite

Experimental alteration of DNA methylation is a suitable tool to infer the relationship between phenotypic and epigenetic variation in plants. A detailed analysis of the genome-wide effect of demethylating agents, such as 5-azacytidine (5azaC), and zebularine is only available for the model species Arabidopsis thaliana, which suggests that 5azaC may have a slightly larger effect. In this study, global methylation estimates obtained by high-performance liquid chromatography (HPLC) analyses were conducted to investigate the impact of 5azaC treatment on leaf and root tissue in Erodium cicutarium (Geraniaceae), which is an annual herb native to Mediterranean Europe that is currently naturalized in all continents, sometimes becoming invasive. We used seeds collected from two natural populations in SE Spain. Root tissue of the second generation (F2) greenhouse-grown seedlings had a significantly lower global cytosine methylation content than leaf tissue (13.0 vs. 17.7% of all cytosines). Leaf tissue consistently decreased methylation after treatment, but the response of root tissue varied according to seed provenance, suggesting that genetic background can mediate the response to experimental demethylation. We also found that both leaf number and leaf length were reduced in treated seedlings supporting a consistent phenotypic effect of the treatment regardless of seedling provenance. These findings suggest that, although the consequences of experimental demethylation may be tissue-and background-specific, this method is effective in altering early seedling development, and can thus be useful in ecological epigenetic studies that are aiming to investigate the links between epigenetic and phenotypic variation in non-model plant species.

show abstract

Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine

Cited by 115 publications

References 60 publications

Light signaling controls nuclear architecture reorganization during seedling establishment

Light signaling controls nuclear architecture reorganization during seedling establishment

Distinct modes of DNA accessibility in plant chromatin

Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

Contact Info

Product

Resources

About