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Epigenomes
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Features Papers in Epigenomes 2025
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Features Papers in Epigenomes 2025

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 570

Special Issue Editors

Dr. Ivana De la Serna

E-Mail Website
Guest Editor
Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
Interests: SWI/SNF chromatin remodeling enzymes; melanocyte differentiation and regulation of pigementation; epigenetic regulation of the response to ultraviolet radiation; cancer epigenetics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Che-Kun James Shen

E-Mail Website
Guest Editor
Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
Interests: gene regulation; chromatin; DNA methylation; neurofunction; transcription
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to collect high-quality papers in the epigenetics and epigenomics research fields. We encourage researchers from various fields within the journal’s scope to contribute papers highlighting the latest developments in their research field or to invite relevant experts and colleagues to do so. The topics of this Special Issue include, but are not limited to, the following:

  • Functional epigenomic studies;
  • Genome-wide epigenetic status and regulation of cells or tissues;
  • Chromatin modifications and remodeling in diseases;
  • Epigenetics in physical diseases;
  • Environmental changes in the epigenetic status of cells or tissues;
  • Inheritance or fixation of epigenetic characteristics;
  • Description of novel methods to study epigenetic regulation;
  • Novel tools, protocols, and technologies for epigenetic studies and therapeutics;
  • Long noncoding RNA (LncRNA), microRNA (miR), and chromatin crosstalk.

Dr. Ivana De la Serna
Prof. Dr. Che-Kun James Shen
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

  • epigenomic
  • epigenetic
  • chromatin modification
  • DNA methylation
  • DNA methyltransferases
  • cancer epigenetics
  • histones

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

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22 pages, 2660 KiB  
Article
Arabidopsis thaliana Roots Exposed to Extracellular Self-DNA: Evidence of Epigenetic Effects
by Alessia Ronchi, Guido Incerti, Emanuele De Paoli, Speranza Claudia Panico, Giovanni Luca Sciabbarrasi, Pasquale Termolino, Fabrizio Cartenì, Mariachiara Langella, Maria Luisa Chiusano and Stefano Mazzoleni
Epigenomes 2025, 9(2), 13; https://doi.org/10.3390/epigenomes9020013 - 30 Apr 2025
Abstract
Background: Previous evidence demonstrated DNA methylation changes in response to stress in plants, showing rapid changes within a limited time frame. Exposure to self-DNA inhibits seedling root elongation, and it was shown that it causes changes in CG DNA methylation in Lactuca sativa [...] Read more.
Background: Previous evidence demonstrated DNA methylation changes in response to stress in plants, showing rapid changes within a limited time frame. Exposure to self-DNA inhibits seedling root elongation, and it was shown that it causes changes in CG DNA methylation in Lactuca sativa. We assessed cytosine methylation changes and associated gene expression patterns in roots of Arabidopsis thaliana Col-0 seedlings exposed to self-DNA for 6 and 24 h. Methods: We used whole genome bisulfite sequencing (WGBS) and RNA-seq analyses to assess genomic cytosine methylation and corresponding gene expression, respectively, on DNA and RNA extracted with commercial kits from roots exposed to self-DNA by an original setup. Fifteen hundred roots replicates, including the control in distilled water, were collected after exposure. Sequencing was performed on a NovaSeq 6000 platform and Ultralow Methyl-Seq System for RNA and DNA WGBS, respectively. Results: Gene expression in roots exposed to self-DNA differed from that of untreated controls, with a total of 305 genes differentially expressed and 87 ontologies enriched in at least one treatment vs. control comparison, and particularly after 24 h of exposure. DNA methylation, particularly in CHG and CHH contexts, was also different, with hyper- and hypomethylation prevailing in treatments vs. controls at 6 h and 24 h, respectively. Differentially expressed genes (DEGs) analysis, Gene Ontology (GO) enrichment analysis, and differentially methylated regions (DMRs) analysis, provided an integrated understanding of the changes associated with self-DNA exposure. Our results suggest differential gene expression associated with DNA methylation in response to self-DNA exposure in A. thaliana roots, enhanced after prolonged exposure. Conclusions: Main functional indications of association between DNA methylation and gene expression involved hypomethylation and downregulation of genes related to nucleotide/nucleoside metabolism (ATP synthase subunit) and cell wall structure (XyG synthase), consistent with previous observations from metabolomics and physiological studies. Further confirmation of these findings will contribute to improving our understanding of the plant molecular response to self-DNA and its implications in stress responses. Full article
(This article belongs to the Special Issue Features Papers in Epigenomes 2025)
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Review

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13 pages, 514 KiB  
Review
Induction of DNA Demethylation: Strategies and Consequences
by Pietro Salvatore Carollo and Viviana Barra
Epigenomes 2025, 9(2), 11; https://doi.org/10.3390/epigenomes9020011 - 12 Apr 2025
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Abstract
DNA methylation is an important epigenetic modification with a plethora of effects on cells, ranging from the regulation of gene transcription to shaping chromatin structure. Notably, DNA methylation occurs thanks to the activity of DNA methyltransferases (DNMTs), which covalently add a methyl group [...] Read more.
DNA methylation is an important epigenetic modification with a plethora of effects on cells, ranging from the regulation of gene transcription to shaping chromatin structure. Notably, DNA methylation occurs thanks to the activity of DNA methyltransferases (DNMTs), which covalently add a methyl group to the cytosine in position 5′ in CpG dinucleotides. Different strategies have been developed to study the effects of DNA methylation in cells, involving either DNMTs inhibition (passive DNA demethylation) or the use of Ten-eleven translocation protein (TET) family enzymes, which directly demethylate DNA (active DNA demethylation). In this manuscript, we will briefly cover the most commonly used strategies in the last two decades to achieve DNA demethylation, along with their effects on cells. We will also discuss some of the newest inducible ways to inhibit DNMTs without remarkable side effects, as well as the effect of non-coding RNAs on DNA methylation. Lastly, we will briefly examine the use of DNA methylation inhibition in biomedical research. Full article
(This article belongs to the Special Issue Features Papers in Epigenomes 2025)
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