Stress-induced structural changes in plant chromatin

Probst, Aline V.; Scheid, Ortrun Mittelsten

doi:10.1016/j.pbi.2015.05.011

Cited by 161 publications

(103 citation statements)

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“…While chromatin states are a critical part of transcriptional responses during development (reviewed in He et al, 2011;Holec and Berger, 2012;Grimanelli and Roudier, 2013;Pikaard and Mittelsten Scheid, 2014;Xiao and Wagner, 2015) or in response to the environment (reviewed in Baulcombe and Dean, 2014;Bond and Baulcombe, 2014;Pikaard and Mittelsten Scheid, 2014;Probst and Mittelsten Scheid, 2015;Vriet et al, 2015), they also play critical roles in creating order in the genome, allowing for the maintenance of proper transcription and genome stability in the face of varying TE landscapes and polyploid changes. We suggest that diverse plant species have evolved variations in the specific mechanisms of chromatin regulation that have allowed them to survive the repeated transposon bursts or polyploidy fusions.…”

Section: Resultsmentioning

confidence: 99%

“…In some cases, chromatin modifiers are likely to be recruited to achieve and stabilize alterations in transcription. Several recent reviews have provided excellent summaries of these activities and point toward the conservation of these pathways among flowering plants (Baulcombe and Dean, 2014;Bond and Baulcombe, 2014;Pikaard and Mittelsten Scheid, 2014;Probst and Mittelsten Scheid, 2015;Vriet et al, 2015;Xiao and Wagner, 2015). In this Review, we focus on aspects of chromatin regulation that might be variable or drive variation among closely related species.…”

Section: Introductionmentioning

confidence: 99%

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Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Springer

Lisch

2016

Plant Cell

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ORCID IDs: 0000-0002-7301-4759 (N.M.S.); 0000-0003-3232-9479 (Q.L.)Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Springer

Lisch

2016

Plant Cell

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“…Thousands of genes are involved in the response; therefore, global genome regulation at the chromatin level is required to achieve the appropriate level of responsiveness (Y. Probst and Mittelsten Scheid, 2015). This may be achieved by nucleosome remodeling and repositioning via covalent modifications of histone proteins, especially trimethylation of histone H3 lysine 4 (van Dijk et al, 2010;Kim et al, 2008) and redistribution of histone variants.…”

Section: Introductionmentioning

confidence: 99%

Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes

et al. 2017

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The influence of the histone variant H2A.Z on transcription remains a long-standing conundrum. Here, by analyzing the actinrelated protein6 mutant, which is impaired in H2A.Z deposition, and by H2A.Z profiling in stress conditions, we investigated the impact of this histone variant on gene expression in Arabidopsis thaliana. We demonstrate that the arp6 mutant exhibits anomalies in response to osmotic stress. Indeed, stress-responsive genes are overrepresented among those hyperactive in arp6. In wild-type plants, these genes exhibit high levels of H2A.Z in the gene body. Furthermore, we observed that in droughtresponsive genes, levels of H2A.Z in the gene body correlate with transcript levels. H2A.Z occupancy, but not distribution, changes in parallel with transcriptional changes. In particular, we observed H2A.Z loss upon transcriptional activation and H2A.Z gain upon repression. These data suggest that H2A.Z has a repressive role in transcription and counteracts unwanted expression in noninductive conditions. However, reduced activity of some genes in arp6 is associated with distinct behavior of H2A.Z at their +1 nucleosome, which exemplifies the requirement of this histone for transcription. Our data support a model where H2A.Z in gene bodies has a strong repressive effect on transcription, whereas in +1 nucleosomes, it is important for maintaining the activity of some genes.

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“…Additionally, repeated exposure to stress can lead to plant stress priming, whereby prior stress exposure conveys an enhanced ability to respond to future events (Conrath et al, 2006;Ding et al, 2012;Gordon et al, 2013;Sani et al, 2013;Wang et al, 2014;Virlouvet and Fromm, 2015;Hilker et al, 2016;Wibowo et al, 2016). This notion has been extended to numerous considerations of the formation of plant stress memory, in which a state of altered stress responsivity is mitotically or meiotically transmissible (Bruce et al, 2007;Hauser et al, 2011b;Probst and Mittelsten Scheid, 2015;Crisp et al, 2016;van Loon, 2016). There is much interest in plant stress memory, including the underlying molecular mechanism(s) and its potential to impact crop yields, particularly in harsh and variable environments (Springer, 2013;Ji et al, 2015;Mickelbart et al, 2015).…”

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confidence: 99%

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

et al. 2017

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Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epialleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.

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Stress-induced structural changes in plant chromatin

Cited by 161 publications

References 110 publications

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

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