Special Issue "Plant Epigenetics"

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

Deadline for manuscript submissions: closed (31 October 2018).

Special Issue Editor

Prof. Dr. José M. Leitão
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Guest Editor
FCT, MeditBio, Universidade do Algarve, Campus de Gambelas, 8005‐139 Faro, Portugal
Interests: molecular biology; plant genetics; plant genomics; plant biotechnology; plant breeding; molecular breeding; genotyping; epigenetics; plant tissue culture; genetic diversity; molecular markers development; plant disease resistance; marker assisted selection; legumes; linkage analysis; experimental mutagenesis; DNA repair; plant cytogenetics
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Special Issue Information

Dear Colleagues,

The open access journal Epigenomes is now accepting submissions for a Special Issue on "Plant Epigenetics". This Special Issue is Guest-Edited by Prof. José Leitão from the University of Algarve, and will include commissioned topical reviews written by leaders in the field. Accepted papers are published online shortly after copy editing.

With each passing day epigenetics unveils its major role in regulation of gene expression.

Epigenetic mechanisms, particularly via small RNAs, histone modifications and DNA methylation, regulate plant development, interaction of plants with biotic and abiotic stresses, plant adaptation to different climates and to changing environmental conditions, often via epigenetic memory and participation of other priming mechanisms.

Involved in silencing of virus and transposable elements the plant epigenetic defense mechanisms are also implicated in transgene silencing.

Impacting plant phenotypes, the epigenetic modifications can give rise to variability useful for plant breeding and to unusual phenomena as paramutation.

This Special Issue will consider research or methodological manuscripts of exceptional interest in the broad field of plant epigenetics, particularly on the following topics:

  • Molecular mechanisms of plant epigenetics
  • Epigenetics and plant gene regulation
  • Epigenetics and plant adaptation to a changing environment
  • Epigenetics and plant response to biotic stresses
  • Priming and epigenetic memory
  • Epigenetics and plant breeding
  • Paramutation and paramutation-like phenomena

Do not miss out on the deadline for submissions: 31 October 2018.

Please use the online submission system and select the Special Issue “Plant Epigenetics”. If you would like to enquire about the suitability of your article for this Special Issue, please email your pre-submission enquiry to Prof. José Leitão at [email protected] with the Epigenomes editorial office [email protected] in copy.

Prof. Dr. José M. Leitão
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 papers will be 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 1400 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.

Published Papers (3 papers)

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Research

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Article
Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance
Epigenomes 2019, 3(1), 4; https://doi.org/10.3390/epigenomes3010004 - 18 Jan 2019
Cited by 8 | Viewed by 2577
Abstract
Chromatin structure, DNA methylation, and histone modifications act in a concerted manner to influence gene expression and therefore plant phenotypes. Environmental stresses are often associated with extensive chromatin rearrangements and modifications of epigenetic levels and patterns. Stress-tolerant plants can be a good tool [...] Read more.
Chromatin structure, DNA methylation, and histone modifications act in a concerted manner to influence gene expression and therefore plant phenotypes. Environmental stresses are often associated with extensive chromatin rearrangements and modifications of epigenetic levels and patterns. Stress-tolerant plants can be a good tool to unveil potential connections between specific epigenetic modifications and stress tolerance capacity. We analyzed genome wide DNA methylation of a salt-tolerant rice variety under salinity and identified a set of differentially methylated regions (DMRs) between control and stress samples using high-throughput sequencing of DNA immunoprecipitated with the 5-methylcytosine antibody (MeDIP-Seq). The examination of DNA methylation pattern at DMRs regions revealed a general tendency for demethylation events in stress samples as compared to control. In addition, DMRs appear to influence the expression of genes located in their vicinity. We hypothesize that short regions as DMRs can shape the chromatin landscape of specific genomic regions and, therefore, may modulate the function of several genes. In this sense, the identification of DMRs represents one step towards to uncover new players in the regulation of stress-responsive genes and new target genes with potential application in enhancement of plant salinity-tolerance. Full article
(This article belongs to the Special Issue Plant Epigenetics)
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Article
Biotic Stress-Induced Priming and De-Priming of Transcriptional Memory in Arabidopsis and Apple
Epigenomes 2019, 3(1), 3; https://doi.org/10.3390/epigenomes3010003 - 14 Jan 2019
Cited by 3 | Viewed by 3391
Abstract
Under natural growth conditions, plants experience various and repetitive biotic and abiotic stresses. Salicylic acid (SA) is a key phytohormone involved in the response to biotic challenges. Application of synthetic SA analogues can efficiently prime defense responses, and leads to improved pathogen resistance. [...] Read more.
Under natural growth conditions, plants experience various and repetitive biotic and abiotic stresses. Salicylic acid (SA) is a key phytohormone involved in the response to biotic challenges. Application of synthetic SA analogues can efficiently prime defense responses, and leads to improved pathogen resistance. Because SA analogues can result in long-term priming and memory, we identified genes for which expression was affected by the SA analogue and explored the role of DNA methylation in this memorization process. We show that treatments with an SA analogue can lead to long-term transcriptional memory of particular genes in Arabidopsis. We found that subsequent challenging of such plants with a bacterial elicitor reverted this transcriptional memory, bringing their expression back to the original pre-treatment level. We also made very similar observations in apple (Malus domestica), suggesting that this expression pattern is highly conserved in plants. Finally, we found a potential role for DNA methylation in the observed transcriptional memory behavior. We show that plants defective in DNA methylation pathways displayed a different memory behavior. Our work improves our understanding of the role of transcriptional memory in priming, and has important implication concerning the application of SA analogues in agricultural settings. Full article
(This article belongs to the Special Issue Plant Epigenetics)
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Review

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Review
How to Design a Whole-Genome Bisulfite Sequencing Experiment
Epigenomes 2018, 2(4), 21; https://doi.org/10.3390/epigenomes2040021 - 11 Dec 2018
Cited by 2 | Viewed by 3665
Abstract
Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of adenine bases. DNA methylation [...] Read more.
Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of adenine bases. DNA methylation can be found in both prokaryotes and eukaryotes. In the latter, dynamic variation is shown across species, along development, and by cell type. DNA methylation usually leads to a lower binding affinity of DNA-interacting proteins and often results in a lower expression rate of the subsequent genome region, a process also referred to as transcriptional gene silencing. We give an overview of the current state of research facilitating the planning and implementation of whole-genome bisulfite-sequencing (WGBS) experiments. We refrain from discussing alternative methods for DNA methylation analysis, such as reduced representation bisulfite sequencing (rrBS) and methylated DNA immunoprecipitation sequencing (MeDIPSeq), which have value in specific experimental contexts but are generally disadvantageous compared to WGBS. Full article
(This article belongs to the Special Issue Plant Epigenetics)
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