Special Issue "DNA Methylation in Plants"

A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: 30 May 2020.

Special Issue Editors

Prof. Dr. Emidio Albertini
E-Mail Website
Guest Editor
Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
Interests: plant reproduction; epigenetics; apomixis; stresses; tomato; grape
Prof. Dr. Cinzia Comino
E-Mail Website
Guest Editor
Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Torino, Italy
Interests: plant genomics; epigenetics; secondary metabolites

Special Issue Information

Dear Colleagues,

The open access journal Plants is now accepting submissions for a Special Issue on "DNA Methylation in Plants". This Special Issue will include commissioned topical reviews written by experts in the field. Accepted papers are published online shortly after copy editing.

Methylation is one of the most studied and mechanistically understood epigenetic modifications, and it is well-conserved among plant, animal, and fungal models. Specifically, plant DNA methylation results in the conversion of the cytosine to N4- or N5-methylcytosine or of the adenine to N6-methyladenine. Changes in the methylation status of these cytosine and adenine residues in genomic DNA play a pivotal role in the regulation of genome functions. In fact, DNA methylation, in combination with histone modifications and non-histone proteins, defines chromatin structure and accessibility, and therefore helps to regulate many molecular processes, such as gene expression, transposon silencing, chromosome interactions, and trait inheritance. Indeed, methylation patterns along a gene can have specific effects on the gene expression: body-methylated genes tend to be constitutively expressed, whereas promoter-methylated genes are preferentially expressed in a tissue-specific manner.

For these reasons, plants use DNA methylation and demethylation to rapidly adapt to environmental changes or to counteract biotic and abiotic stresses.

The forthcoming Special Issue aims to provide an overview of recent studies regarding DNA methylation in plants, particularly on the DNA methylation and demethylation dynamics associated with

  • plant development;
  • key biological process regulation (e.g., leaf growth, seed development, heterosis, fruit ripening);
  • synthesis of secondary metabolites; and
  • response to biotic and abiotic stresses.

Moreover, studies on genes involved in plant DNA methylation and in its regulation will be also considered.

Do not miss out on the deadline for submissions: 31 May 2020.

Please use the online submission system and select the Special Issue “DNA Methylation in Plants”.

Prof. Dr. Emidio Albertini
Prof. Dr. Cinzia Comino
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 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. Plants is an international peer-reviewed open access monthly 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 1600 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

  • DNA methylation
  • gene regulation
  • transposon silencing
  • plant development
  • epigenetics
  • 5mC
  • 6mA

Published Papers (2 papers)

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Research

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Open AccessArticle
Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa
Plants 2019, 8(12), 526; https://doi.org/10.3390/plants8120526 - 20 Nov 2019
Abstract
Histone modifications, such as methylation and demethylation, are vital for regulating chromatin structure, thus affecting its expression patterns. The objective of this study is to understand the phylogenetic relationships, genomic organization, diversification of motif modules, gene duplications, co-regulatory network analysis, and expression dynamics [...] Read more.
Histone modifications, such as methylation and demethylation, are vital for regulating chromatin structure, thus affecting its expression patterns. The objective of this study is to understand the phylogenetic relationships, genomic organization, diversification of motif modules, gene duplications, co-regulatory network analysis, and expression dynamics of histone lysine methyltransferases and histone demethylase in Brassica rapa. We identified 60 SET (HKMTases), 53 JmjC, and 4 LSD (HDMases) genes in B. rapa. The domain composition analysis subcategorized them into seven and nine subgroups, respectively. Duplication analysis for paralogous pairs of SET and JmjC (eight and nine pairs, respectively) exhibited variation. Interestingly, three pairs of SET exhibited Ka/Ks > 1.00 values, signifying positive selection, whereas the remaining underwent purifying selection with values less than 1.00. Furthermore, RT-PCR validation analysis and RNA-sequence data acquired on six different tissues (i.e., leaf, stem, callus, silique, flower, and root) revealed dynamic expression patterns. This comprehensive study on the abundance, classification, co-regulatory network analysis, gene duplication, and responses to heat and cold stress of SET and JmjC provides insights into the structure and diversification of these family members in B. rapa. This study will be helpful to reveal functions of these putative SET and JmjC genes in B. rapa. Full article
(This article belongs to the Special Issue DNA Methylation in Plants)
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Review

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Open AccessReview
DNA N6-Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code
Plants 2020, 9(2), 247; https://doi.org/10.3390/plants9020247 - 14 Feb 2020
Abstract
N6-methyladenine (6mA) is a DNA base modification at the 6th nitrogen position; recently, it has been resurfaced as a potential reversible epigenetic mark in eukaryotes. Despite its existence, 6mA was considered to be absent due to its undetectable level. However, with [...] Read more.
N6-methyladenine (6mA) is a DNA base modification at the 6th nitrogen position; recently, it has been resurfaced as a potential reversible epigenetic mark in eukaryotes. Despite its existence, 6mA was considered to be absent due to its undetectable level. However, with the new advancements in methods, considerable 6mA distribution is identified across the plant genome. Unlike 5-methylcytosine (5mC) in the gene promoter, 6mA does not have a definitive role in repression but is exposed to have divergent regulation in gene expression. Though 6mA information is less known, the available evidences suggest its function in plant development, tissue differentiation, and regulations in gene expression. The current review article emphasizes the research advances in DNA 6mA modifications, identification, available databases, analysis tools and its significance in plant development, cellular functions and future perspectives of research. Full article
(This article belongs to the Special Issue DNA Methylation in Plants)

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type: Review

Title: DNA N6-Methyladenine Modification in Plant Genomes – A Glimpse into Emerging Epigenetic Code

Abstract: Methylation of adenine (6mA) is a DNA base modification at the 6th position of nitrogen; recently, it’s been resurfaced as a potential reversible epigenetic mark in Eukaryotes.  Despite its existence, 6mA was considered to be absent due to the undetectable level. However, new advancements in methods, considerable distribution are identified across the plant genome.  Unlike 5-methylcytosine (5mC) methylation in the gene promoter, 6mA is not having a definitive role in repression but exposed to have divergent regulation in gene expression. Though 6mA information is naive, the available evidence demonstrates that indispensable function in plant development, DNA replication, tissue differentiation, and regulations in gene expression. The current review article is emphasis the research advances in DNA 6mA modifications, identification, and its significance in plant development, cellular functions and future perspectives of research.

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