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Epigenomes
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Epigenetic Control in Plants
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Epigenetic Control in Plants

A topical collection in Epigenomes (ISSN 2075-4655).

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Editor

Dr. Vladimir Brukhin

E-Mail Website
Collection Editor
Department of Plant Embryology & Reproductive Biology, Komarov Botanical Institute RAS, 2 Professor Popov Street, 197376 Saint-Petersburg, Russia
Interests: development; sexual and asexual reproduction; genomics
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

Plants are sessile organisms with the capacity to respond to a varying environment throughout their lives. This capability is mediated through the moderation of gene expression without change to DNA sequence, a phenomenon known as epigenetics.  Epigenetic mechanisms thereby mediate developmental progression of an organism and also the resilience to accommodate for change.  Thus, epigenetic regulation in plants can be mediated in several ways, most notably mi RNA- and siRNA-based systems, histone modification and DNA methylation.

On a global scale methylation accumulates during somatic development, although external stimuli can cause either the methylation or demethylation of specific sites. About a third of plant genes are methylated at maturity but meiosis acts as a clearing house for methylation, with only a few methylated sites surviving through to the next generation. Atypical methylation can cause developmental or physiological anomalies.

The aim of this Topic Collection is to bring together a set of reviews and research articles on the role of epigenetic regulation in plants during sexual and asexual reproduction, development, and evolution.

Dr. Vladimir Brukhin
Collection Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Epigenomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1500 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • epigenetics
  • methylation
  • RNA interference
  • chromatin remodeling
  • plant reproduction
  • development

Published Papers (5 papers)

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2024

Jump to: 2023, 2021, 2020

17 pages, 3119 KiB  
Article
Transcription Factors Are Involved in Wizened Bud Occurrence During the Growing Season in the Pyrus pyrifolia Cultivar ‘Sucui 1’
by Hui Li, Jialiang Kan, Chunxiao Liu, Qingsong Yang, Jing Lin and Xiaogang Li
Epigenomes 2024, 8(4), 40; https://doi.org/10.3390/epigenomes8040040 - 25 Oct 2024
Viewed by 428
Abstract
Background: Flowers are important plant organs, and their development is correlated with yield in woody fruit trees. For Pyrus pyrifolia cultivar ‘Sucui 1’, the research on how DNA methylation accurately regulates the expression of TFs and affects the specific regulatory mechanism of flower [...] Read more.
Background: Flowers are important plant organs, and their development is correlated with yield in woody fruit trees. For Pyrus pyrifolia cultivar ‘Sucui 1’, the research on how DNA methylation accurately regulates the expression of TFs and affects the specific regulatory mechanism of flower bud wizening will help reduce wizened buds. Methods: Here, the DNA methylomes and transcriptomes of two types of flower buds from the Pyrus pyrifolia cultivar ‘Sucui 1’ were compared. Results: 320 differentially expressed transcription factors (TFs), in 43 families, were obtained from the wizened bud transcriptome versus the normal bud transcriptome. Most were members of the AP2/ERF, bHLH, C2H2, CO-like, MADS, MYB, and WRKY families, which are involved in flower development. As a whole, the methylation level of TFs in the ‘Sucui 1’ genome increased once flower bud wizening occurred. A cytosine methylation analysis revealed that the methylation levels of the same gene regions in TFs from two kinds of buds were similar. However, differentially methylated regions were found in gene promoter sequences. The combined whole-genome bisulfite sequencing and RNA-Seq analyses revealed 162 TF genes (including 164 differentially methylated regions) with both differential expression and methylation differences between the two flower bud types. Among them, 126 were classified as mCHH-type methylation genes. Furthermore, the transcriptional down regulation of PpbHLH40, PpERF4, PpERF061, PpLHW, PpMADS6, PpZF-HD11, and PpZFP90 was accompanied by increased DNA methylation. However, PpbHLH130, PpERF011, and PpMYB308 displayed the opposite trend. The expression changes for these TFs were negatively correlated with their methylation states. Conclusions: Overall, our results offer initial experimental evidence of a correlation between DNA methylation and TF transcription in P. pyrifolia in response to bud wizening. This enriched our understanding of epigenetic modulations in woody trees during flower development. Full article
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10 pages, 1727 KiB  
Article
α-Crystalline Domains and Intrinsically Disordered Regions Can Work in Parallel to Induce Accumulation of MBD6 at Chromocenters in Arabidopsis thaliana
by Brandon A. Boone, Cristy P. Mendoza, Noah J. Behrendt and Steven E. Jacobsen
Epigenomes 2024, 8(3), 33; https://doi.org/10.3390/epigenomes8030033 - 28 Aug 2024
Viewed by 795
Abstract
Proteins are localized and concentrated at cellular and genomic locations for specific and efficient functions. Efforts to understand protein accumulation in eukaryotic organisms have primarily focused on multivalent interactions between intrinsically disordered regions (IDRs) as mediators of protein condensation. We previously showed that [...] Read more.
Proteins are localized and concentrated at cellular and genomic locations for specific and efficient functions. Efforts to understand protein accumulation in eukaryotic organisms have primarily focused on multivalent interactions between intrinsically disordered regions (IDRs) as mediators of protein condensation. We previously showed that α-crystalline domain (ACD) proteins 15 (ACD15) and 21 (ACD21) were required for multimerization and the accumulation of gene-silencing methyl-CpG-binding domain protein 6 (MBD6) at chromocenters in Arabidopsis thaliana. Here, we demonstrate that ACDs and IDRs can act as parallel mechanisms, facilitating higher-order MBD6 assemblies. Using human IDRs known to be important for protein accumulation, we replicated and enhanced the accumulation of MBD6 at chromocenters. In addition, IDRs fused to MBD6 could substitute for ACD function and partially reconstitute the MBD6 gene-silencing function. However, the accumulation of MBD6 by IDRs still required ACD15 and ACD21 for full effect. These results establish that ACD-mediated protein accumulation is a mechanism that can function similarly to and together with IDR-mediated mechanisms. Full article
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2023

Jump to: 2024, 2021, 2020

19 pages, 740 KiB  
Review
The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants
by Carlos de Tomás and Carlos M. Vicient
Epigenomes 2024, 8(1), 2; https://doi.org/10.3390/epigenomes8010002 - 27 Dec 2023
Cited by 3 | Viewed by 2782
Abstract
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, [...] Read more.
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a “genomic shock” that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms. Full article
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2021

Jump to: 2024, 2023, 2020

14 pages, 1608 KiB  
Review
Epigenetic Modifications in Plant Development and Reproduction
by Vladimir Brukhin and Emidio Albertini
Epigenomes 2021, 5(4), 25; https://doi.org/10.3390/epigenomes5040025 - 19 Nov 2021
Cited by 12 | Viewed by 5602
Abstract
Plants are exposed to highly fluctuating effects of light, temperature, weather conditions, and many other environmental factors throughout their life. As sessile organisms, unlike animals, they are unable to escape, hide, or even change their position. Therefore, the growth and development of plants [...] Read more.
Plants are exposed to highly fluctuating effects of light, temperature, weather conditions, and many other environmental factors throughout their life. As sessile organisms, unlike animals, they are unable to escape, hide, or even change their position. Therefore, the growth and development of plants are largely determined by interaction with the external environment. The success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addition to how environmental factors can change the patterns of genes expression, epigenetic regulation determines how genetic expression changes during the differentiation of one cell type into another and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many ‘epigenomes’. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction when epigenetic marks are eliminated during meiosis and early embryogenesis and later reappear. However, during asexual plant reproduction, when meiosis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adaptive significance. In asexuals, epigenetic regulation is of particular importance for imparting plasticity to the phenotype when, apart from mutations, the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review. Full article
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2020

Jump to: 2024, 2023, 2021

1 pages, 140 KiB  
Editorial
Epigenetic Control in Plants
by Vladimir Brukhin
Epigenomes 2020, 4(3), 11; https://doi.org/10.3390/epigenomes4030011 - 1 Jul 2020
Viewed by 2658
Abstract
Epigenetic regulation in plants is an exciting field of research [...] Full article
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