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Epigenomes
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A Commemorative Issue in Honor of the 30th Anniversary of...
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A Commemorative Issue in Honor of the 30th Anniversary of the Epigenetics Society

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 6534

Special Issue Editors

Dr. Humaira Gowher

E-Mail Website
Guest Editor
Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
Interests: cell culture; gene expression; DNA sequencing; genomics; gene regulation; next generation sequencing; epigenetics; regulation of gene expression; transcription; transcriptional regulation; DNA methylation; gene expression and chromatin biology; chromatin; methylation; histone modification; epigenomics; ChIP-sequencing; chromatin remodeling; chromatin structure; chromatin biology; embryonic stem cell culture and differentiation; enhancer regulation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Assam El-Osta

E-Mail Website
Guest Editor
Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
Interests: diabetes; clinical and molecular epigenetics; chromatin; DNA and RNA methylation; histones; transcriptional regulation; computational epigenomics; metabolic disease
Special Issues, Collections and Topics in MDPI journals
Dr. Andrea Fuso

E-Mail Website
Guest Editor
Department of Experimental Medicine, Sapienza University of Rome, 00185 Roma, Italy
Interests: DNA methylation; epigenetics; nutrition; methylation metabolism; environmental epigenetics; neuroepigenetics; gene expression and chromatin biology; bisulfite sequencing; real-time PCR; Alzheimer’s disease; aging research; beta amyloid; neuroscience; neurobiology; neurodegenerative diseases; neurophysiology; neurodegeneration; neurobiology and brain physiology; animal models; cell culture; neurobiochemistry; methylation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Epigenetics Society (ES) was originally founded as the DNA Methylation Society (DMS) in March 1994. One of the reasons for establishing the ES was the reluctance of many molecular biologists to recognize the major importance of DNA methylation for the regulation of normal and pathological gene expression. In 2006, as the larger field of epigenetics was growing exponentially, we renamed DMS to the Epigenetics Society.

In 2023, the ES updated its website and organized the 1st ES International Meeting in Rome. More than 200 attendees from over 20 countries all over the world attended the meeting at which there were talks and posters presenting results related to the major aspects of epigenetics. Although the epigenetics (and DNA methylation) literature is still undergoing exponential growth, there is not enough awareness among biologists and the medical profession of the importance of epigenetics for health and the biosphere. The mission of the ES continues to be encouraging epigenetics researchers, facilitating interactions between them and helping educate the lay public and scientists in general about the importance of epigenetics.

We invite the epigenetics research community to submit Research or Review manuscripts for this ES 30th Anniversary Special Issue of Epigenomes, an open access journal. We welcome submissions from established members of the ES, recently joined members (https://epigeneticssocietyint.com/) and attendees at the Rome ES meeting.  This Special Issue aims to gather high-quality research manuscripts on any aspect of epigenetic research. This includes basic, applied and translational research. Potential topics are DNA methylation and hydroxymethylation, histone modifications, higher-order chromatin structure, non-coding RNAs, epigenetics of development, epigenetics of cancer and other diseases, epigenetics of aging, plant and invertebrate epigenetics, environmental epigenetics, novel epigenetic technologies, the biochemical and molecular basis of epigenetics, and readers and writers of epigenetics. 

Dr. Humaira Gowher
Prof. Dr. Assam El-Osta
Dr. Andrea Fuso
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

  • epigenetics
  • DNA methylation
  • histone modifications
  • chromatin remodeling
  • ncRNAs
  • chromatin architecture
  • insulators
  • enhancers

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Published Papers (4 papers)

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Research

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18 pages, 4934 KiB  
Article
Associations between Circulating Biomarkers of One-Carbon Metabolism and Mitochondrial D-Loop Region Methylation Levels
by Andrea Stoccoro, Martina Lari, Lucia Migliore and Fabio Coppedè
Epigenomes 2024, 8(4), 38; https://doi.org/10.3390/epigenomes8040038 - 9 Oct 2024
Cited by 1 | Viewed by 1148
Abstract
Background/Objectives: One-carbon metabolism is a critical pathway for epigenetic mechanisms. Circulating biomarkers of one-carbon metabolism have been associated with changes in nuclear DNA methylation levels in individuals affected by age-related diseases. More and more studies are showing that even mitochondrial DNA (mtDNA) could [...] Read more.
Background/Objectives: One-carbon metabolism is a critical pathway for epigenetic mechanisms. Circulating biomarkers of one-carbon metabolism have been associated with changes in nuclear DNA methylation levels in individuals affected by age-related diseases. More and more studies are showing that even mitochondrial DNA (mtDNA) could be methylated. In particular, methylation of the mitochondrial displacement (D-loop) region modulates the gene expression and replication of mtDNA and, when altered, can contribute to the development of human illnesses. However, no study until now has demonstrated an association between circulating biomarkers of one-carbon metabolism and D-loop methylation levels. Methods: In the study presented herein, we searched for associations between circulating one-carbon metabolism biomarkers, including folate, homocysteine, and vitamin B12, and the methylation levels of the D-loop region in DNA obtained from the peripheral blood of 94 elderly voluntary subjects. Results: We observed a positive correlation between D-loop methylation and vitamin B12 (r = 0.21; p = 0.03), while no significant correlation was observed with folate (r = 0.02; p = 0.80) or homocysteine levels (r = 0.02; p = 0.82). Moreover, D-loop methylation was increased in individuals with high vitamin B12 levels compared to those with normal vitamin B12 levels (p = 0.04). Conclusions: This is the first study suggesting an association between vitamin B12 circulating levels and mtDNA methylation in human subjects. Given the potential implications of altered one-carbon metabolism and mitochondrial epigenetics in human diseases, a deeper understanding of their interaction could inspire novel interventions with beneficial effects for human health. Full article
(This article belongs to the Special Issue A Commemorative Issue in Honor of the 30th Anniversary of the Epigenetics Society)
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Review

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15 pages, 1022 KiB  
Review
PHF8/KDM7B: A Versatile Histone Demethylase and Epigenetic Modifier in Nervous System Disease and Cancers
by Tingyu Fan, Jianlian Xie, Guo Huang, Lili Li, Xi Zeng and Qian Tao
Epigenomes 2024, 8(3), 36; https://doi.org/10.3390/epigenomes8030036 - 15 Sep 2024
Viewed by 1305
Abstract
Many human diseases, such as malignant tumors and neurological diseases, have a complex pathophysiological etiology, often accompanied by aberrant epigenetic changes including various histone modifications. Plant homologous domain finger protein 8 (PHF8), also known as lysine-specific demethylase 7B (KDM7B), is a critical histone [...] Read more.
Many human diseases, such as malignant tumors and neurological diseases, have a complex pathophysiological etiology, often accompanied by aberrant epigenetic changes including various histone modifications. Plant homologous domain finger protein 8 (PHF8), also known as lysine-specific demethylase 7B (KDM7B), is a critical histone lysine demethylase (KDM) playing an important role in epigenetic modification. Characterized by the zinc finger plant homology domain (PHD) and the Jumonji C (JmjC) domain, PHF8 preferentially binds to H3K4me3 and erases repressive methyl marks, including H3K9me1/2, H3K27me1, and H4K20me1. PHF8 is indispensable for developmental processes and the loss of PHF8 enzyme activity is linked to neurodevelopmental disorders. Moreover, increasing evidence shows that PHF8 is highly expressed in multiple tumors as an oncogenic factor. These findings indicate that studying the role of PHF8 will facilitate the development of novel therapeutic agents by the manipulation of PHF8 demethylation activity. Herein, we summarize the current knowledge of PHF8 about its structure and demethylation activity and its involvement in development and human diseases, with an emphasis on nervous system disorders and cancer. This review will update our understanding of PHF8 and promote the clinical transformation of its predictive and therapeutic value. Full article
(This article belongs to the Special Issue A Commemorative Issue in Honor of the 30th Anniversary of the Epigenetics Society)
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18 pages, 2094 KiB  
Review
Epigenetic Regulation of Mammalian Cardiomyocyte Development
by Isaiah K. Mensah and Humaira Gowher
Epigenomes 2024, 8(3), 25; https://doi.org/10.3390/epigenomes8030025 - 29 Jun 2024
Viewed by 1494
Abstract
The heart is the first organ formed during mammalian development and functions to distribute nutrients and oxygen to other parts of the developing embryo. Cardiomyocytes are the major cell types of the heart and provide both structural support and contractile function to the [...] Read more.
The heart is the first organ formed during mammalian development and functions to distribute nutrients and oxygen to other parts of the developing embryo. Cardiomyocytes are the major cell types of the heart and provide both structural support and contractile function to the heart. The successful differentiation of cardiomyocytes during early development is under tight regulation by physical and molecular factors. We have reviewed current studies on epigenetic factors critical for cardiomyocyte differentiation, including DNA methylation, histone modifications, chromatin remodelers, and noncoding RNAs. This review also provides comprehensive details on structural and morphological changes associated with the differentiation of fetal and postnatal cardiomyocytes and highlights their differences. A holistic understanding of all aspects of cardiomyocyte development is critical for the successful in vitro differentiation of cardiomyocytes for therapeutic purposes. Full article
(This article belongs to the Special Issue A Commemorative Issue in Honor of the 30th Anniversary of the Epigenetics Society)
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Other

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9 pages, 2649 KiB  
Opinion
Keep Fingers on the CpG Islands
by Xing Zhang, Robert M. Blumenthal and Xiaodong Cheng
Epigenomes 2024, 8(2), 23; https://doi.org/10.3390/epigenomes8020023 - 19 Jun 2024
Viewed by 1777
Abstract
The post-genomic era has ushered in the extensive application of epigenetic editing tools, allowing for precise alterations of gene expression. The use of reprogrammable editors that carry transcriptional corepressors has significant potential for long-term epigenetic silencing for the treatment of human diseases. The [...] Read more.
The post-genomic era has ushered in the extensive application of epigenetic editing tools, allowing for precise alterations of gene expression. The use of reprogrammable editors that carry transcriptional corepressors has significant potential for long-term epigenetic silencing for the treatment of human diseases. The ideal scenario involves precise targeting of a specific genomic location by a DNA-binding domain, ensuring there are no off-target effects and that the process yields no genetic remnants aside from specific epigenetic modifications (i.e., DNA methylation). A notable example is a recent study on the mouse Pcsk9 gene, crucial for cholesterol regulation and expressed in hepatocytes, which identified synthetic zinc-finger (ZF) proteins as the most effective DNA-binding editors for silencing Pcsk9 efficiently, specifically, and persistently. This discussion focuses on enhancing the specificity of ZF-array DNA binding by optimizing interactions between specific amino acids and DNA bases across three promoters containing CpG islands. Full article
(This article belongs to the Special Issue A Commemorative Issue in Honor of the 30th Anniversary of the Epigenetics Society)
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