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Advances in Molecular Mechanisms of Plant Epigenetics
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Advances in Molecular Mechanisms of Plant Epigenetics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (28 March 2023) | Viewed by 4406

Special Issue Editor

Dr. Konstantinos E. Vlachonasios

E-Mail Website
Guest Editor
Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
Interests: histone acetylation; plant development; plant molecular genetics; epigenetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Epigenetic mechanisms are defined as potentially heritable changes in gene expression that do not involve alteration in the underlying DNA sequence, such as DNA methylation, histone modifications, chromatin alterations, and the activity of non-coding RNAs. They have a decisive function in regulating plant growth and development, as well as plant responses to the environment. Furthermore, epigenetic processes significantly impact plant development and the heritability of multiple plant traits. The involvement of epigenetic mechanisms in plant biology has been documented. Understanding how epigenetic regulation is involved in plant growth, development, and response to environmental stress is highly desirable, not only for a better understanding of the molecular mechanisms of plant responses to developmental or environmental cues, but also for possible applications in the genetic manipulation of plants. The proposed topic is focused on molecular mechanisms of epigenetic regulation of plants. We welcome all types of articles (original research, methods, opinions, and reviews) that provide new insight into different aspects of plant epigenetic mechanisms, including their regulation, their function in plant development, their function in plant responses to abiotic and biotic stresses, and their function in epigenomic variation, using models or crop plants.

Dr. Konstantinos E. Vlachonasios
Guest 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 special issue 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. Plants is an international peer-reviewed open access semimonthly 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 2700 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
  • DNA methylation
  • histone modification
  • non-coding RNA
  • chromatin remodeling
  • histone variants
  • plant growth
  • plant development
  • plant abiotic stress
  • plant biotic stress
  • epigenome
  • priming
  • epigenetic variation

Published Papers (2 papers)

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Research

15 pages, 2220 KiB  
Article
The Chromatin Remodeling Factor BrCHR39 Targets DNA Methylation to Positively Regulate Apical Dominance in Brassica rapa
by Wei Zhu, Zhengqing Xie, Zhenni Chu, Yakun Ding, Gongyao Shi, Weiwei Chen, Xiaochun Wei, Yuxiang Yuan, Fang Wei and Baoming Tian
Plants 2023, 12(6), 1384; https://doi.org/10.3390/plants12061384 - 20 Mar 2023
Cited by 1 | Viewed by 1381
Abstract
The SHPRH (SNF2, histone linker, PHD, RING, helicase) subfamily belonging to ATP-dependent chromatin remodeling factor is the effective tumor-suppressor, which can polyubiquitinate PCNA (proliferating cell nuclear antigen) and participate in post-replication repair in human. However, little is known about the functions of SHPRH [...] Read more.
The SHPRH (SNF2, histone linker, PHD, RING, helicase) subfamily belonging to ATP-dependent chromatin remodeling factor is the effective tumor-suppressor, which can polyubiquitinate PCNA (proliferating cell nuclear antigen) and participate in post-replication repair in human. However, little is known about the functions of SHPRH proteins in plants. In this study, we identified a novel SHPRH member BrCHR39 and obtained BrCHR39-silenced transgenic Brassica rapa. In contrast to wild-type plants, transgenic Brassica plants exhibited a released apical dominance phenotype with semi-dwarfism and multiple lateral branches. Furthermore, a global alteration of DNA methylation in the main stem and bud appeared after silencing of BrCHR39. Based on the GO (gene ontology) functional annotation and KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis, the plant hormone signal transduction pathway was clearly enriched. In particular, we found a significant increase in the methylation level of auxin-related genes in the stem, whereas auxin- and cytokinin-related genes were hypomethylated in the bud of transgenic plants. In addition, further qRT-PCR (quantitative real-time PCR) analysis revealed that DNA methylation level always had an opposite trend with gene expression level. Considered together, our findings indicated that suppression of BrCHR39 expression triggered the methylation divergence of hormone-related genes and subsequently affected transcription levels to regulate the apical dominance in Brassica rapa. Full article
(This article belongs to the Special Issue Advances in Molecular Mechanisms of Plant Epigenetics)
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16 pages, 2523 KiB  
Article
ADA2b and GCN5 Affect Cytokinin Signaling by Modulating Histone Acetylation and Gene Expression during Root Growth of Arabidopsis thaliana
by Foteini Tsilimigka, Stylianos Poulios, Areti Mallioura and Konstantinos Vlachonasios
Plants 2022, 11(10), 1335; https://doi.org/10.3390/plants11101335 - 18 May 2022
Cited by 6 | Viewed by 2602
Abstract
In Arabidopsis thaliana, the histone acetyltransferase GCN5 and the associated coactivator ADA2b regulate root growth and affect gene expression. The cytokinin signaling reporter TCS::GFP was introduced into gcn5-1, ada2b-1, and ada2a-2, as well as the ada2a-2ada2b-1 mutants. [...] Read more.
In Arabidopsis thaliana, the histone acetyltransferase GCN5 and the associated coactivator ADA2b regulate root growth and affect gene expression. The cytokinin signaling reporter TCS::GFP was introduced into gcn5-1, ada2b-1, and ada2a-2, as well as the ada2a-2ada2b-1 mutants. The early root growth (4 to 7 days post-germination) was analyzed using cellular and molecular approaches. TCS signal accumulated from the fourth to seventh days of root growth in the wild-type columella cells. In contrast, ada2b-1 and gcn5-1 and ada2a-2ada2b-1 double mutants displayed reduced TCS expression relative to wild type. Gene expression analysis showed that genes associated with cytokinin homeostasis were downregulated in the roots of gcn5-1 and ada2b-1 mutants compared to wild-type plants. H3K14 acetylation was affected in the promoters of cytokinin synthesis and catabolism genes during root growth of Arabidopsis. Therefore, GCN5 and ADA2b are positive regulators of cytokinin signaling during root growth by modulating histone acetylation and the expression of genes involved in cytokinin synthesis and catabolism. Auxin application in the roots of wild-type seedlings increased TCS::GFP expression. In contrast, ada2b and ada2ada2b mutant plants do not show the auxin-induced TCS signal, suggesting that GCN5 and ADA2b are required for the auxin-induced cytokinin signaling in early root growth. Full article
(This article belongs to the Special Issue Advances in Molecular Mechanisms of Plant Epigenetics)
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