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Epigenomes
Special Issues
Mechanisms of Plant Epigenome Dynamics
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Mechanisms of Plant Epigenome Dynamics

A special issue of Epigenomes (ISSN 2075-4655).

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 29041

Special Issue Editors

Dr. Clara Richet-Bourbousse

E-Mail Website
Guest Editor
Institut de Biologie de l’Ecole Nnormale Supérieure (IBENS), 75005 Paris, France
Interests: chromatin mechanisms of transcription regulation; nuclear organization; plant adaptation to light; chloroplast signaling; functional links between metabolism and chromatin
Special Issues, Collections and Topics in MDPI journals
Dr. Sandra Fonseca

E-Mail Website
Guest Editor
Centro Nacional de Biotecnologia (CNB) - CSIC, 28049 Madrid, Spain
Interests: plant adaptation to the environment; light signaling; protein homeostasis; changes in chromatin states and transcription factor stability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Open Access journal Epigenomes is now accepting submissions for a Special Issue on “Mechanisms of Plant Epigenome Dynamics”.

Plants constantly adapt to their local environment thanks to their remarkable phenotypic plasticity. Over recent years, it has become apparent that the signaling pathways driving these morphological and physiological changes, in adaptation to biotic or abiotic stimuli, often converge to chromatin-based mechanisms. Gene expression and silencing, but also DNA repair and replication, are impacted by the structure of the chromatin fiber, nucleosome positioning and composition, histone modifications, DNA methylation, non-coding RNAs, and, at a wider scale, localization in the nuclear space.

Big advances have been made in characterizing the regulators involved in chromatin modifications and mechanistic links with different plant signaling components have begun to emerge. Such mechanisms notably include the control of certain chromatin modifiers’ stability and of the genomic regions where they are recruited, and the control of specific histone variants’ expression. Understanding the molecular mechanisms governing chromatin dynamics and their functional outcome at the cellular and organismal levels will be key to improve plant resilience to environmental conditions while ensuring good developmental performances.

This Special Issue will be focused on the mechanisms of plant epigenome dynamics. We will consider reviews, research, or method manuscripts of exceptional interest on the following topics:

  • chromatin modifiers and remodelers;
  • histone variants;
  • histone modifications and DNA methylation;
  • non-coding RNAs;
  • chromatin compartmentalization and 3D organization.

The described mechanistic aspects of chromatin variations can relate, but are not restricted, to:

  • epigenetic silencing;
  • DNA replication and repair;
  • transcriptional regulations;
  • epigenetic memory and chromatin priming;
  • vegetative and reproductive plant development;
  • cell fate, phenotypic plasticity, and phase transitions;
  • environmental adaptations;
  • epigenetics for better crops.

Dr. Clara Bourbousse
Dr. Sandra Fonseca
Guest Editors

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. 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

  • plant epigenomics
  • chromatin modifiers and remodelers
  • DNA methylation
  • histone modifications
  • histone variants
  • 3D genome.

Published Papers (6 papers)

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Research

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17 pages, 4453 KiB  
Article
Advanced Image Analysis Methods for Automated Segmentation of Subnuclear Chromatin Domains
by Philippe Johann to Berens, Geoffrey Schivre, Marius Theune, Jackson Peter, Salimata Ousmane Sall, Jérôme Mutterer, Fredy Barneche, Clara Bourbousse and Jean Molinier
Epigenomes 2022, 6(4), 34; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes6040034 - 05 Oct 2022
Cited by 1 | Viewed by 2761
Abstract
The combination of ever-increasing microscopy resolution with cytogenetical tools allows for detailed analyses of nuclear functional partitioning. However, the need for reliable qualitative and quantitative methodologies to detect and interpret chromatin sub-nuclear organization dynamics is crucial to decipher the underlying molecular processes. Having [...] Read more.
The combination of ever-increasing microscopy resolution with cytogenetical tools allows for detailed analyses of nuclear functional partitioning. However, the need for reliable qualitative and quantitative methodologies to detect and interpret chromatin sub-nuclear organization dynamics is crucial to decipher the underlying molecular processes. Having access to properly automated tools for accurate and fast recognition of complex nuclear structures remains an important issue. Cognitive biases associated with human-based curation or decisions for object segmentation tend to introduce variability and noise into image analysis. Here, we report the development of two complementary segmentation methods, one semi-automated (iCRAQ) and one based on deep learning (Nucl.Eye.D), and their evaluation using a collection of A. thaliana nuclei with contrasted or poorly defined chromatin compartmentalization. Both methods allow for fast, robust and sensitive detection as well as for quantification of subtle nucleus features. Based on these developments, we highlight advantages of semi-automated and deep learning-based analyses applied to plant cytogenetics. Full article
(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)
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Review

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21 pages, 1171 KiB  
Review
The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors
by James Godwin and Sara Farrona
Epigenomes 2022, 6(1), 8; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes6010008 - 03 Mar 2022
Cited by 15 | Viewed by 6020
Abstract
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from [...] Read more.
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation. Full article
(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)
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29 pages, 28969 KiB  
Review
Polycomb Repressive Complex 2 in Eukaryotes—An Evolutionary Perspective
by Mallika Vijayanathan, María Guadalupe Trejo-Arellano and Iva Mozgová
Epigenomes 2022, 6(1), 3; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes6010003 - 17 Jan 2022
Cited by 10 | Viewed by 5843
Abstract
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals [...] Read more.
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution. Full article
(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)
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11 pages, 651 KiB  
Review
The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator
by Tajbir Raihan, Robert L. Geneve, Sharyn E. Perry and Carlos M. Rodriguez Lopez
Epigenomes 2021, 5(4), 24; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5040024 - 18 Oct 2021
Cited by 10 | Viewed by 4449
Abstract
In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase [...] Read more.
In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress. Full article
(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)
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11 pages, 1328 KiB  
Review
Evolution of CG Methylation Maintenance Machinery in Plants
by Louis Tirot, Pauline E. Jullien and Mathieu Ingouff
Epigenomes 2021, 5(3), 19; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5030019 - 14 Sep 2021
Cited by 9 | Viewed by 4082
Abstract
Cytosine methylation is an epigenetic mark present in most eukaryotic genomes that contributes to the regulation of gene expression and the maintenance of genome stability. DNA methylation mostly occurs at CG sequences, where it is initially deposited by de novo DNA methyltransferases and [...] Read more.
Cytosine methylation is an epigenetic mark present in most eukaryotic genomes that contributes to the regulation of gene expression and the maintenance of genome stability. DNA methylation mostly occurs at CG sequences, where it is initially deposited by de novo DNA methyltransferases and propagated by maintenance DNA methyltransferases (DNMT) during DNA replication. In this review, we first summarize the mechanisms maintaining CG methylation in mammals that involve the DNA Methyltransferase 1 (DNMT1) enzyme and its cofactor, UHRF1 (Ubiquitin-like with PHD and RING Finger domain 1). We then discuss the evolutionary conservation and diversification of these two core factors in the plant kingdom and speculate on potential functions of novel homologues typically observed in land plants but not in mammals. Full article
(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)
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16 pages, 1468 KiB  
Review
Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering
by Annick Dubois and François Roudier
Epigenomes 2021, 5(3), 17; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5030017 - 24 Aug 2021
Cited by 7 | Viewed by 4334
Abstract
CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss [...] Read more.
CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation. Full article
(This article belongs to the Special Issue Mechanisms of Plant Epigenome Dynamics)
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