The Epigenome and Plant Development

He, Guangming; Elling, Axel A.; Deng, Xing Wang

doi:10.1146/annurev-arplant-042110-103806

Cited by 165 publications

(123 citation statements)

References 150 publications

(293 reference statements)

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“…Hundreds of light-responsive genes are rapidly subjected to local chromatin state variations during this transition (reviewed in refs. [36][37][38]. Establishment of transcriptionally permissive chromatin states at hundreds of light-inducible genes by acetylation and methylation of histone H3 at specific residues (e.g., H3K9ac and H3K4me3) and ubiquitination of histone H2B are associated with gene induction (39)(40)(41)(42), and this is notably required for their optimal up-regulation (39).…”

Section: Significancementioning

confidence: 99%

Light signaling controls nuclear architecture reorganization during seedling establishment

Bourbousse

Mestiri

Zabulon

et al. 2015

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

108

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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,

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Section: Significancementioning

confidence: 99%

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

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“…In addition to DNA sequence modifications, it has been shown that epigenetic variations contribute to genome accessibility, functionality and structure 16,17 . Several studies have demonstrated that local DNA methylation variants, which are represented by differential cytosine methylation at particular loci, can have major effects on the transcription of nearby genes and can be inherited over generations [18][19][20] .…”

mentioning

confidence: 99%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

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Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

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“…Accordingly, rapid changes in the gene expression patterns that accompany SE induction have been reported in various plants (Elhiti et al 2013) including Arabidopsis (Gliwicka et al 2013;Wickramasuriya and Dunwell 2015). The reprogramming of the cell transcriptome that results in the release of a new developmental programme is associated with extensive changes in the chromatin structure, which involves chemical modifications of DNA and histones (He et al 2011a;De-la-Peña et al 2015;Mozgová et al 2017). Among the epigenetic modifications that control gene expression, the methylation of DNA is considered to play a pivotal role in plant development (Zhang et al 2010;Turck and Coupland 2014;Victoria et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

et al. 2018

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Epigenetic processes including DNA methylation play a pivotal role in regulating the genes that control plant development. In contrast to in planta development, the contribution of DNA methylation to the morphogenic processes that are induced in vitro are much less recognised. Hence, in the present study, we analysed the impact of DNA methylation on somatic embryogenesis (SE) that was induced in Arabidopsis. The results demonstrated a decrease in the global DNA methylation level during SE that contrasted with the up-regulation of MET1 and CMT3 DNA methylases and the down-regulation of DNA demethylases (ROS1, DME and DML2). Hence, the global DNA methylation level appears not to correlate with the transcriptional activity of the genes encoding DNA methylases/demethylases, thereby implying the complexity of the regulatory mechanism that controls the DNA methylation status of the SE-epigenome. Moreover, distinct changes in the expression level of the SE-regulatory genes were indicated in the 5-AzaC-treated and DNA methylase mutant cultures. Accordingly, a significant repression of the LEC2, LEC1 and BBM genes was found in the 5-AzaC-treated culture that was incapable of SE induction. In contrast, the distinct up-regulation of these genes was observed in the drm1drm2 and drm1drm2cmt3 mutant cultures with an improved embryogenic response. The modulated expression of DNA methylase genes and the significantly modified embryogenic response of the met1 and drm mutants imply that both the maintenance and the de novo pathway of DNA methylation are engaged in the regulation of SE in Arabidopsis.

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The Epigenome and Plant Development

Cited by 165 publications

References 150 publications

Light signaling controls nuclear architecture reorganization during seedling establishment

Light signaling controls nuclear architecture reorganization during seedling establishment

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

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