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Epigenomes
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DNA Methylation Markers in Health and Disease
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DNA Methylation Markers in Health and Disease

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

Deadline for manuscript submissions: 31 May 2026 | Viewed by 838

Special Issue Editor

Dr. Osman El‐Maarri

E-Mail Website
Guest Editor
Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, 53127 Bonn, Germany
Interests: epigenetics and human disease; DNA methylation; epigenetic biomarkers; repetitive DNA; F8 intracellular trafficking; endothelial cells

Special Issue Information

Dear Colleagues,

This Special Issue, “DNA Methylation Markers in Health and Disease”, aims to explore the critical role of DNA methylation as a biomarker in physiological and pathological processes. DNA methylation, a key epigenetic mechanism, regulates gene expression and genomic stability, influencing development, aging, and disease progression. This issue will highlight advances in identifying methylation-based biomarkers for early diagnosis, prognosis, and therapeutic monitoring in cancer, neurological disorders, cardiovascular diseases, and other conditions. We invite original research, reviews, and methodological studies that investigate novel methylation signatures, their functional implications, and clinical applications. Contributions may also address technological innovations in methylation profiling, bioinformatics tools, and the integration of epigenomic data with other omics layers. By compiling cutting-edge research, this Special Issue seeks to enhance the understanding of DNA methylation's role in health and disease, fostering translational breakthroughs for precision medicine.

Dr. Osman El‐Maarri
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 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 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
  • epigenetic biomarkers
  • disease diagnostics
  • precision medicine
  • methylation profiling

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Published Papers (2 papers)

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Research

14 pages, 657 KB  
Article
Comparative Mapping of N6-Methyladenine, C5-Methylcytosine, and C5-Hydroxymethylcytosine in a Single Species Reveals Constitutive, Somatic- and Germline-Specific, and Age-Related Genomic Context Distributions and Biological Functions
by Thibaut Renard and Serge Aron
Epigenomes 2025, 9(3), 35; https://doi.org/10.3390/epigenomes9030035 - 18 Sep 2025
Abstract
Background/Objectives: The DNA methylome allows environmental signals to be converted into stable and adaptive changes in gene expression. While 5-methylcytosine (5mC) has been extensively studied, alternative epigenetic marks such as N6-methyladenine (6mA) and 5-hydroxymethylcytosine (5hmC) remain poorly understood. Comparative studies of these marks [...] Read more.
Background/Objectives: The DNA methylome allows environmental signals to be converted into stable and adaptive changes in gene expression. While 5-methylcytosine (5mC) has been extensively studied, alternative epigenetic marks such as N6-methyladenine (6mA) and 5-hydroxymethylcytosine (5hmC) remain poorly understood. Comparative studies of these marks are rare, and their results are often confounded by phylogeny, tissue type, developmental stage, or methodology. Here, we aimed to disentangle the constitutive, somatic- and germline-specific, and/or age-related patterns displayed by 6mA, 5mC, and 5hmC within a single species. Methods: We generated long-read nanopore sequencing data for somatic tissues of buff-tailed bumblebee (Bombus terrestris) males and their sperm, enabling simultaneous detection of 6mA, 5mC, and 5hmC. We used a stepwise approach to successively identify (i) constitutive patterns conserved between somatic tissues and sperm, (ii) differences between the soma and the germline, and (iii) age-related changes between young and old males. Results: We found distinct constitutive, somatic and sperm, and age-related specific signatures in the genomic contexts, maintenance fidelity, and biological functions associated with 6mA, 5mC, and 5hmC. Sperm cells consistently displayed lower methylation entropy than did somatic tissues, indicating more stable methylation patterns in the germline. 5mC exhibited the greatest variation across all genomic contexts; 6mA and 5hmC displayed less dramatic differences. The influence of age was subtler but revealed context-dependent remodeling of methylation, particularly for 5hmC. Conclusions: We observed that 6mA, 5mC, and 5hmC displayed constitutive, somatic- and sperm-specific, and age-related differences that were associated with distinct genomic contexts and biological functions, supporting the complementarity of these methylation marks and their diverging epigenetic roles. Full article
(This article belongs to the Special Issue DNA Methylation Markers in Health and Disease)
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20 pages, 2861 KB  
Article
DNA Methylation Status of Regulatory Regions of Apoptosis-Associated Genes in Dystropy «Huntington’s Disease—Non-Small Cell Lung Cancer»
by Nadezhda P. Babushkina, Elena Yu. Bragina, Densema E. Gomboeva, Iuliia A. Koroleva, Sergey N. Illarioshkin, Sergey A. Klyushnikov, Nataliya Yu. Abramycheva, Maria A. Nikitina, Valentina M. Alifirova, Nikolai V. Litviakov, Marina K. Ibragimova, Matvey M. Tsyganov, Irina A. Tsydenova, Aleksei A. Zarubin, Irina A. Goncharova, Maria V. Golubenko, Ramil R. Salakhov, Aleksei A. Sleptcov, Aksana N. Kucher, Maria S. Nazarenko and Valery P. Puzyrevadd Show full author list remove Hide full author list
Epigenomes 2025, 9(3), 28; https://doi.org/10.3390/epigenomes9030028 - 7 Aug 2025
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Abstract
Background. Studies of comorbid (syntropic) and inversely comorbid (rarely occurring together, i.e., dystropic) diseases have focused on the search for molecular causes of this phenomenon. Materials. We investigated DNA methylation levels in regulatory regions of 23 apoptosis-associated genes as candidate loci associated with [...] Read more.
Background. Studies of comorbid (syntropic) and inversely comorbid (rarely occurring together, i.e., dystropic) diseases have focused on the search for molecular causes of this phenomenon. Materials. We investigated DNA methylation levels in regulatory regions of 23 apoptosis-associated genes as candidate loci associated with the “cancer–neurodegeneration” dystropy in patients with Huntington’s disease (HD) and patients with non–small cell lung cancer (LC). Results. Statistically significant differences in methylation levels between the HD and LC groups were found for 41 CpG sites in 16 genes. The results show that five genes (SETDB1, TWIST1, HDAC1, SP1, and GRIA2) are probably involved in the phenomenon of inverse comorbidity of these diseases. For these genes, the methylation levels of the studied CpG sites were altered in opposite directions in the two groups of patients, compared to the control group. Conclusions. For the SP1 gene, the above hypothesis is supported by our analysis of open-access data on gene expression in patients with the aforementioned diagnoses and fits a probable mechanism of the “HD–LC” dystropy. Full article
(This article belongs to the Special Issue DNA Methylation Markers in Health and Disease)
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