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DNA Methylation in Plants
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DNA Methylation in Plants

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

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 21697

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
Special Issues, Collections and Topics in MDPI journals
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 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

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

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Published Papers (6 papers)

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Research

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18 pages, 2872 KiB  
Article
Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula
by Jose Carballo, Diego Zappacosta, Gianpiero Marconi, Jimena Gallardo, Marco Di Marsico, Cristian A. Gallo, Mario Caccamo, Emidio Albertini and Viviana Echenique
Plants 2021, 10(5), 946; https://doi.org/10.3390/plants10050946 - 10 May 2021
Cited by 7 | Viewed by 3163
Abstract
DNA methylation is an epigenetic mechanism by which a methyl group is added to a cytosine or an adenine. When located in a gene/regulatory sequence it may repress or de-repress genes, depending on the context and species. Eragrostis curvula is an apomictic grass [...] Read more.
DNA methylation is an epigenetic mechanism by which a methyl group is added to a cytosine or an adenine. When located in a gene/regulatory sequence it may repress or de-repress genes, depending on the context and species. Eragrostis curvula is an apomictic grass in which facultative genotypes increases the frequency of sexual pistils triggered by epigenetic mechanisms. The aim of the present study was to look for correlations between the reproductive mode and specific methylated genes or genomic regions. To do so, plants with contrasting reproductive modes were investigated through MCSeEd (Methylation Context Sensitive Enzyme ddRad) showing higher levels of DNA methylation in apomictic genotypes. Moreover, an increased proportion of differentially methylated positions over the regulatory regions were observed, suggesting its possible role in regulation of gene expression. Interestingly, the methylation pathway was also found to be self-regulated since two of the main genes (ROS1 and ROS4), involved in de-methylation, were found differentially methylated between genotypes with different reproductive behavior. Moreover, this work allowed us to detect several genes regulated by methylation that were previously found as differentially expressed in the comparisons between apomictic and sexual genotypes, linking DNA methylation to differences in reproductive mode. Full article
(This article belongs to the Special Issue DNA Methylation in Plants)
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24 pages, 3392 KiB  
Article
Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum
by Mariano Soliman, Maricel Podio, Gianpiero Marconi, Marco Di Marsico, Juan Pablo A. Ortiz, Emidio Albertini and Luciana Delgado
Plants 2021, 10(4), 793; https://doi.org/10.3390/plants10040793 - 17 Apr 2021
Cited by 6 | Viewed by 2955
Abstract
Apomixis seems to emerge from the deregulation of preexisting genes involved in sexuality by genetic and/or epigenetic mechanisms. The trait is associated with polyploidy, but diploid individuals of Paspalum rufum can form aposporous embryo sacs and develop clonal seeds. Moreover, diploid hybrid families [...] Read more.
Apomixis seems to emerge from the deregulation of preexisting genes involved in sexuality by genetic and/or epigenetic mechanisms. The trait is associated with polyploidy, but diploid individuals of Paspalum rufum can form aposporous embryo sacs and develop clonal seeds. Moreover, diploid hybrid families presented a wide apospory expressivity variation. To locate methylation changes associated with apomixis expressivity, we compare relative DNA methylation levels, at CG, CHG, and CHH contexts, between full-sib P. rufum diploid genotypes presenting differential apospory expressivity. The survey was performed using a methylation content-sensitive enzyme ddRAD (MCSeEd) strategy on samples at premeiosis/meiosis and postmeiosis stages. Based on the relative methylation level, principal component analysis and heatmaps, clearly discriminate samples with contrasting apospory expressivity. Differential methylated contigs (DMCs) showed 14% of homology to known transcripts of Paspalum notatum reproductive transcriptome, and almost half of them were also differentially expressed between apomictic and sexual samples. DMCs showed homologies to genes involved in flower growth, development, and apomixis. Moreover, a high proportion of DMCs aligned on genomic regions associated with apomixis in Setaria italica. Several stage-specific differential methylated sequences were identified as associated with apospory expressivity, which could guide future functional gene characterization in relation to apomixis success at diploid and tetraploid levels. Full article
(This article belongs to the Special Issue DNA Methylation in Plants)
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13 pages, 1264 KiB  
Article
DNA Modification Patterns within the Transposable Elements of the Fig (Ficus carica L.) Genome
by Gabriele Usai, Alberto Vangelisti, Samuel Simoni, Tommaso Giordani, Lucia Natali, Andrea Cavallini and Flavia Mascagni
Plants 2021, 10(3), 451; https://doi.org/10.3390/plants10030451 - 27 Feb 2021
Cited by 16 | Viewed by 3028
Abstract
Transposable element activity can be harmful to the host’s genome integrity, but it can also provide selective advantages. One strategy to cope with transposons is epigenetic control through DNA base modifications. We report the non-canonic DNA modification dynamics of fig (Ficus carica [...] Read more.
Transposable element activity can be harmful to the host’s genome integrity, but it can also provide selective advantages. One strategy to cope with transposons is epigenetic control through DNA base modifications. We report the non-canonic DNA modification dynamics of fig (Ficus carica L.) by exploiting high-quality genome reference and related N4-methylcytosine (4mC) and N6-methyladenine (6mA) data. Overall, 1.49% of transposon nucleotides showed either 4mC or 6mA modifications: the 4mC/6mA ratio was similar in Class I and Class II transposons, with a prevalence of 4mC, which is comparable to coding genes. Different percentages of 4mC or 6mA were observed among LTR-retrotransposon lineages and sub-lineages. Furthermore, both the Copia and Gypsy retroelements showed higher modification rates in the LTR and coding regions compared with their neighbour regions. Finally, the unconventional methylation of retrotransposons is unrelated to the number of close genes, suggesting that the 4mC and 6mA frequency in LTR-retrotransposons should not be related to transcriptional repression in the adjacency of the element. In conclusion, this study highlighted unconventional DNA modification patterns in fig transposable elements. Further investigations will focus on functional implications, in regards to how modified retroelements affect the expression of neighbouring genes, and whether these epigenetic markers can spread from repeats to genes, shaping the plant phenotype. Full article
(This article belongs to the Special Issue DNA Methylation in Plants)
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10 pages, 1837 KiB  
Article
Fungal Infection Induces Anthocyanin Biosynthesis and Changes in DNA Methylation Configuration of Blood Orange [Citrus sinensis L. (Osbeck)]
by Angelo Sicilia, Vittoria Catara, Emanuele Scialò and Angela Roberta Lo Piero
Plants 2021, 10(2), 244; https://doi.org/10.3390/plants10020244 - 27 Jan 2021
Cited by 16 | Viewed by 2605
Abstract
The biosynthesis of sweet orange anthocyanins is triggered by several environmental factors such as low temperature. Much less is known about the effect of biotic stress on anthocyanin production in sweet orange, although in other species anthocyanins are often indicated as “defense molecules”. [...] Read more.
The biosynthesis of sweet orange anthocyanins is triggered by several environmental factors such as low temperature. Much less is known about the effect of biotic stress on anthocyanin production in sweet orange, although in other species anthocyanins are often indicated as “defense molecules”. In this work, citrus fruits were inoculated with Penicillium digitatum, the causal agent of green mold, and the amount of anthocyanins and the expression of genes related to their biosynthesis was monitored by RT-real time PCR after 3 and 5 days from inoculation (DPI). Moreover, the status of cytosine methylation of DFR and RUBY promoter regions was investigated by McrBC digestion followed in real-time. Our results highlight that fungal infection induces anthocyanin production by activating the expression of several genes in the biosynthetic pathway. The induction of gene expression is accompanied by maintenance of high levels of methylation at the DFR and RUBY promoters in the inoculated fruits, thus suggesting that DNA methylation is not a repressive mark of anthocyanin related gene expression in sweet orange subjected to biotic stress. Finally, by measuring the expression levels of the Citrus DNA demethylase genes, we found that none of them is up-regulated in response to fungal infection, this result being in accordance with the observed maintenance of high-level DFR and Ruby promoter regions methylation. Full article
(This article belongs to the Special Issue DNA Methylation in Plants)
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19 pages, 3223 KiB  
Article
Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa
by Gaofeng Liu, Nadeem Khan, Xiaoqing Ma and Xilin Hou
Plants 2019, 8(12), 526; https://doi.org/10.3390/plants8120526 - 20 Nov 2019
Cited by 9 | Viewed by 3212
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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12 pages, 883 KiB  
Review
DNA N6-Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code
by Jeyalakshmi Karanthamalai, Aparna Chodon, Shailja Chauhan and Gopal Pandi
Plants 2020, 9(2), 247; https://doi.org/10.3390/plants9020247 - 14 Feb 2020
Cited by 18 | Viewed by 5216
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)
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