Advances in DNA Methylation

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Nucleic Acids".

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 10878

Special Issue Editor


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Guest Editor
Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
Interests: clinical epigenetics (diagnostic and prognostic epi-signatures); EWAS; epigenetic editing (dCAS); epigenetics and machine learning; single-cell analyses
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Special Issue Information

DNA methylation (DNAm) and histone modifications (HMs) are crucial mechanisms governing chromatin architecture and genome stability and are the most commonly studied epigenetic features. The epigenome represents a highly dynamic mechanism controlled by a complex system of proteins involving epigenetic writers, readers, remodelers, and erasers. Genetic variation in genes encoding for such proteins often leads to severe disease or syndromes. On the other hand, it can also be affected by external and environmental factors, which may also lead to or be associated with disease. Epigenetic changes can contribute to the development of numerous diseases, including neurodegenerative, autoimmune diseases, cancer, and noncommunicable and multifactorial diseases. Recent progress in statistical methodology and approaches is paving the way toward deeper insight into the role of epigenetics and related molecular mechanisms within the pathophysiology of disease. Machine learning, network analysis, and multiomics analyses are to date frequently implemented in order to develop a whole new set of diagnostic and prognostic, and basal biology, toolkits. Moreover, since the epigenome is dynamic by definition, epigenetic editing, by means of (d)CAS fusion proteins or by small epigenetically active molecules, seems to be a promising future direction for intervention strategies.

In this Special Issue, we invite you to submit an original research report or review article deciphering the role of DNA methylation in malignancies, aging or differentiation.

Dr. Peter Henneman
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. Biomolecules 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 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
  • Epigenetics
  • Signature
  • epigenetic editing, machine learning.

Published Papers (3 papers)

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Review

28 pages, 2754 KiB  
Review
DNA Methylation in Regulatory T Cell Differentiation and Function: Challenges and Opportunities
by Lu Bai, Xiaolei Hao, Julia Keith and Yongqiang Feng
Biomolecules 2022, 12(9), 1282; https://doi.org/10.3390/biom12091282 - 12 Sep 2022
Cited by 9 | Viewed by 3780
Abstract
As a bona fide epigenetic marker, DNA methylation has been linked to the differentiation and function of regulatory T (Treg) cells, a subset of CD4 T cells that play an essential role in maintaining immune homeostasis and suppressing autoimmunity and antitumor immune response. [...] Read more.
As a bona fide epigenetic marker, DNA methylation has been linked to the differentiation and function of regulatory T (Treg) cells, a subset of CD4 T cells that play an essential role in maintaining immune homeostasis and suppressing autoimmunity and antitumor immune response. DNA methylation undergoes dynamic regulation involving maintenance of preexisting patterns, passive and active demethylation, and de novo methylation. Scattered evidence suggests that these processes control different stages of Treg cell lifespan ranging from lineage induction to cell fate maintenance, suppression of effector T cells and innate immune cells, and transdifferentiation. Despite significant progress, it remains to be fully explored how differential DNA methylation regulates Treg cell fate and immunological function. Here, we review recent progress and discuss the questions and challenges for further understanding the immunological roles and mechanisms of dynamic DNA methylation in controlling Treg cell differentiation and function. We also explore the opportunities that these processes offer to manipulate Treg cell suppressive function for therapeutic purposes by targeting DNA methylation. Full article
(This article belongs to the Special Issue Advances in DNA Methylation)
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26 pages, 2098 KiB  
Review
Role of WTAP in Cancer: From Mechanisms to the Therapeutic Potential
by Yongfei Fan, Xinwei Li, Huihui Sun, Zhaojia Gao, Zheng Zhu and Kai Yuan
Biomolecules 2022, 12(9), 1224; https://doi.org/10.3390/biom12091224 - 2 Sep 2022
Cited by 15 | Viewed by 3701
Abstract
Wilms’ tumor 1-associating protein (WTAP) is required for N6-methyladenosine (m6A) RNA methylation modifications, which regulate biological processes such as RNA splicing, cell proliferation, cell cycle, and embryonic development. m6A is the predominant form of mRNA modification in [...] Read more.
Wilms’ tumor 1-associating protein (WTAP) is required for N6-methyladenosine (m6A) RNA methylation modifications, which regulate biological processes such as RNA splicing, cell proliferation, cell cycle, and embryonic development. m6A is the predominant form of mRNA modification in eukaryotes. WTAP exerts m6A modification by binding to methyltransferase-like 3 (METTL3) in the nucleus to form the METTL3-methyltransferase-like 14 (METTL14)-WTAP (MMW) complex, a core component of the methyltransferase complex (MTC), and localizing to the nuclear patches. Studies have demonstrated that WTAP plays a critical role in various cancers, both dependent and independent of its role in m6A modification of methyltransferases. Here, we describe the recent findings on the structural features of WTAP, the mechanisms by which WTAP regulates the biological functions, and the molecular mechanisms of its functions in various cancers. By summarizing the latest WTAP research, we expect to provide new directions and insights for oncology research and discover new targets for cancer treatment. Full article
(This article belongs to the Special Issue Advances in DNA Methylation)
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16 pages, 361 KiB  
Review
Research Progress of DNA Methylation in Endometrial Cancer
by Ting Xu, Hongmei Ding, Jie Chen, Jiahui Lei, Meng Zhao, Bingyu Ji, Youguo Chen, Songbing Qin and Qinqin Gao
Biomolecules 2022, 12(7), 938; https://doi.org/10.3390/biom12070938 - 4 Jul 2022
Cited by 9 | Viewed by 2839
Abstract
Endometrial cancer (EC)) is one of the most common malignant tumors of the female genital system, with an increasing incidence and mortality, worldwide. Although the therapeutic strategy of EC is still complicated and challenging, further understanding of carcinogenesis from a gene perspective would [...] Read more.
Endometrial cancer (EC)) is one of the most common malignant tumors of the female genital system, with an increasing incidence and mortality, worldwide. Although the therapeutic strategy of EC is still complicated and challenging, further understanding of carcinogenesis from a gene perspective would allow an effort to improve therapeutic precision in this complex malignancy. DNA methylation is the most widely studied epigenetic alteration in human tumors. Aberrant DNA methylation events, resulting in altered gene expression, are features of many tumor types. In this review, we provide an update on evidence about the roles of aberrant DNA methylation within some classical tumor suppressor genes and oncogenes in endometrial carcinogenesis, and report on recent advances in the understanding of the contribution of aberrant DNA methylation to EC, as well as opportunities and challenges of DNA methylation in EC management and prevention. Full article
(This article belongs to the Special Issue Advances in DNA Methylation)
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