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Epigenetics and Chromatin Modifications in Plants

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 10187

Special Issue Editor


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Guest Editor
Institute of Agricultural Biology and Biotechnology, National Research Council, Milan, Italy
Interests: structural and functional genomics; gene expression; DNA methylation; stress response; maize; rice; tomato; common bean

Special Issue Information

Epigenetics and chromatin modifications play an important role in numerous biological processes, including transposable element silencing, gene regulation, response to environmental stimuli, development, and probably also in evolution. Epigenetics can be defined as the heritable patterns of phenotypic variation that cannot exclusively be explained by changes in the DNA sequence. These heritable patterns are part of a complex network of mechanisms that dynamically regulates DNA methylation. Similarly to DNA mutations, the occurrence of epigenetic variation can produce new heritable patterns that can lead to aberrant gene expression and phenotypic variation. In plants, epialleles have been identified for genes that control important traits such as flower morphology, fruit ripening, sex determination, plant size, and tissue pigmentations. Despite the fact that chromatin modifications are not always heritable, they affect important plant processes not involving DNA variations. These chromatin modifications involve biochemical changes such as histones modification. Many aspects of both epigenetics and chromatin modifications still remain unclear. Therefore, it is crucial to update our knowledge with the help of new information regarding these important biological processes.

For this Special Issue of IJMS, we invite you to submit original research reports or review articles deciphering the role of epigenetics and chromatin modifications in plants.

Dr. Raul Pirona
Guest Editor

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Published Papers (3 papers)

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Research

18 pages, 2927 KiB  
Article
Genome-Wide Mapping of Cytosine Methylation Revealed Dynamic DNA Methylation Patterns Associated with Sporophyte Development of Saccharina japonica
by Xiaoqi Yang, Xiuliang Wang, Jianting Yao and Delin Duan
Int. J. Mol. Sci. 2021, 22(18), 9877; https://doi.org/10.3390/ijms22189877 - 13 Sep 2021
Cited by 3 | Viewed by 1895
Abstract
Cytosine methylation plays vital roles in regulating gene expression and plant development. However, the function of DNA methylation in the development of macroalgae remains unclear. Through the genome-wide bisulfite sequencing of cytosine methylation in holdfast, stipe and blade, we obtained the complete 5-mC [...] Read more.
Cytosine methylation plays vital roles in regulating gene expression and plant development. However, the function of DNA methylation in the development of macroalgae remains unclear. Through the genome-wide bisulfite sequencing of cytosine methylation in holdfast, stipe and blade, we obtained the complete 5-mC methylation landscape of Saccharina japonica sporophyte. Our results revealed that the total DNA methylation level of sporophyte was less than 0.9%, and the content of CHH contexts was dominant. Moreover, the distribution of CHH methylation within the genes exhibited exon-enriched characteristics. Profiling of DNA methylation in three parts revealed the diverse methylation pattern of sporophyte development. These pivotal DMRs were involved in cell motility, cell cycle and cell wall/membrane biogenesis. In comparison with stipe and blade, hypermethylation of mannuronate C5-epimerase in holdfast decreased the transcript abundance, which affected the synthesis of alginate, the key component of cell walls. Additionally, 5-mC modification participated in the regulation of blade and holdfast development by the glutamate content respectively via glutamine synthetase and amidophosphoribosyl transferase, which may act as the epigenetic regulation signal. Overall, our study revealed the global methylation characteristics of the well-defined holdfast, stipe and blade, and provided evidence for epigenetic regulation of sporophyte development in brown macroalgae. Full article
(This article belongs to the Special Issue Epigenetics and Chromatin Modifications in Plants)
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23 pages, 6383 KiB  
Article
Expression Patterns of DNA Methylation and Demethylation Genes during Plant Development and in Response to Phytohormones
by Morgan Bennett, Kailyn Cleaves and Tarek Hewezi
Int. J. Mol. Sci. 2021, 22(18), 9681; https://doi.org/10.3390/ijms22189681 - 7 Sep 2021
Cited by 14 | Viewed by 2975
Abstract
DNA methylation and demethylation precisely and effectively modulate gene expression during plant growth and development and in response to stress. However, expression profiles of genes involved in DNA methylation and demethylation during plant development and their responses to phytohormone treatments remain largely unknown. [...] Read more.
DNA methylation and demethylation precisely and effectively modulate gene expression during plant growth and development and in response to stress. However, expression profiles of genes involved in DNA methylation and demethylation during plant development and their responses to phytohormone treatments remain largely unknown. We characterized the spatiotemporal expression patterns of genes involved in de novo methylation, methyl maintenance, and active demethylation in roots, shoots, and reproductive organs using β-glucuronidase (GUS) reporter lines. Promoters of DNA demethylases were generally more highly active at the mature root tissues, whereas the promoters of genes involved in DNA methylation were more highly active at fast-growing root tissues. The promoter activity also implies that methylation status in shoot apex, leaf primordia, floral organs, and developing embryos is under tight equilibrium through the activity of genes involved in DNA methylation and demethylation. The promoter activity of DNA methylation and demethylation-related genes in response to various phytohormone treatments revealed that phytohormones can alter DNA methylation status in specific and redundant ways. Overall, our results illustrate that DNA methylation and demethylation pathways act synergistically and antagonistically in various tissues and in response to phytohormone treatments and point to the existence of hormone-linked methylome regulation mechanisms that may contribute to tissue differentiation and development. Full article
(This article belongs to the Special Issue Epigenetics and Chromatin Modifications in Plants)
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20 pages, 3320 KiB  
Article
DNA Demethylation in Response to Heat Stress in Arabidopsis thaliana
by Urszula Korotko, Karolina Chwiałkowska, Izabela Sańko-Sawczenko and Miroslaw Kwasniewski
Int. J. Mol. Sci. 2021, 22(4), 1555; https://doi.org/10.3390/ijms22041555 - 4 Feb 2021
Cited by 32 | Viewed by 4604
Abstract
Environmental stress is one of the most important factors affecting plant growth and development. Recent studies have shown that epigenetic mechanisms, such as DNA methylation, play a key role in adapting plants to stress conditions. Here, we analyzed the dynamics of changes in [...] Read more.
Environmental stress is one of the most important factors affecting plant growth and development. Recent studies have shown that epigenetic mechanisms, such as DNA methylation, play a key role in adapting plants to stress conditions. Here, we analyzed the dynamics of changes in the level of DNA methylation in Arabidopsis thaliana (L.) Heynh. (Brassicaceae) under the influence of heat stress. For this purpose, whole-genome sequencing of sodium bisulfite-treated DNA was performed. The analysis was performed at seven time points, taking into account the control conditions, heat stress, and recovery to control conditions after the stress treatment was discontinued. In our study we observed decrease in the level of DNA methylation under the influence of heat stress, especially after returning to control conditions. Analysis of the gene ontology enrichment and regulatory pathways showed that genes characterized by differential DNA methylation are mainly associated with stress response, including heat stress. These are the genes encoding heat shock proteins and genes associated with translation regulation. A decrease in the level of DNA methylation in such specific sites suggests that under the influence of heat stress we observe active demethylation phenomenon rather than passive demethylation, which is not locus specific. Full article
(This article belongs to the Special Issue Epigenetics and Chromatin Modifications in Plants)
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