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New Advances in Epigenetics and Epigenomics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 March 2025 | Viewed by 3170

Special Issue Editor


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Guest Editor
School of Medicine and Public Health, The University of Newcastle, Newcastle, Australia
Interests: epigenetics; epigenomics; epitranscriptomics

Special Issue Information

Dear Colleagues,

Epigenetic changes have been implicated in various diseases such as cancer, neurodegenerative conditions, autoimmune disease and cardiovascular disease. Epigenetics refers to heritable changes in gene function that do not involve changes to the underlying DNA sequence, and epigenomics is the study of these changes across the entire genome. In recent years, advances in high-throughput sequencing technology, genome editing and multi-omics analysis have facilitated the study of epigenetic changes. This Special Issue will focus on studies utilizing advances in epigenetics and epigenomics including, but not limited to, single-cell epigenomics, CRISPR-based epigenomic editing, DNA methylation and demethylation dynamics, epitranscriptomics and the integration of epigenomic data with other “omics” fields.

Dr. Vicki Maltby
Guest Editor

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Keywords

  • epigenetics
  • epigenomics
  • multi-omics
  • epitranscriptomics
  • single cell

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Published Papers (3 papers)

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Review

16 pages, 751 KiB  
Review
Study of microRNAs in Gingival Crevicular Fluid as Periodontal Diseases Biomarkers: Systematic Review
by María Cosín-Villanueva, Pedro J. Almiñana-Pastor, Jose Luis García-Giménez and Andrés López-Roldán
Int. J. Mol. Sci. 2024, 25(15), 8274; https://doi.org/10.3390/ijms25158274 - 29 Jul 2024
Viewed by 626
Abstract
Aim: The aim of this review was to identify the microRNAs (miRNAs) present in gingival crevicular fluid (GCF) that can be used as biomarkers for the diagnosis of periodontal diseases, and to determine which of them has a higher diagnostic yield for periodontitis. [...] Read more.
Aim: The aim of this review was to identify the microRNAs (miRNAs) present in gingival crevicular fluid (GCF) that can be used as biomarkers for the diagnosis of periodontal diseases, and to determine which of them has a higher diagnostic yield for periodontitis. Methods: The review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines (reference number CRD42024544648). The Pubmed, Scopus, Cochrane Library, Embase, Web of Science, and Google Scholar databases were searched for clinical studies conducted in humans investigating periodontal diseases and miRNAs in GCF. The methodological quality of the articles was measured with the Newcastle–Ottawa Scale. Results: A total of 3222 references were identified in the initial literature search, and 16 articles were finally included in the review. The design of the studies was heterogeneous, which prevented a meta-analysis of the data. Most of the studies compared miRNA expression levels between patients with periodontitis and healthy controls. The most widely researched miRNA in periodontal diseases was miR-200b-3p and miR-146a. Conclusions: the miRNAs most studied are miR-146a, miR-200b, miR-223, miR-23a, and miR-203, and all of them except miR-203 have an acceptable diagnostic plausibility for periodontitis. Full article
(This article belongs to the Special Issue New Advances in Epigenetics and Epigenomics)
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21 pages, 750 KiB  
Review
Role of HDAC5 Epigenetics in Chronic Craniofacial Neuropathic Pain
by Sifong Elise Hui and Karin N. Westlund
Int. J. Mol. Sci. 2024, 25(13), 6889; https://doi.org/10.3390/ijms25136889 - 23 Jun 2024
Viewed by 720
Abstract
The information provided from the papers reviewed here about the role of epigenetics in chronic craniofacial neuropathic pain is critically important because epigenetic dysregulation during the development and maintenance of chronic neuropathic pain is not yet well characterized, particularly for craniofacial pain. We [...] Read more.
The information provided from the papers reviewed here about the role of epigenetics in chronic craniofacial neuropathic pain is critically important because epigenetic dysregulation during the development and maintenance of chronic neuropathic pain is not yet well characterized, particularly for craniofacial pain. We have noted that gene expression changes reported vary depending on the nerve injury model and the reported sample collection time point. At a truly chronic timepoint of 10 weeks in our model of chronic neuropathic pain, functional groupings of genes examined include those potentially contributing to anti-inflammation, nerve repair/regeneration, and nociception. Genes altered after treatment with the epigenetic modulator LMK235 are discussed. All of these differentials are key in working toward the development of diagnosis-targeted therapeutics and likely for the timing of when the treatment is provided. The emphasis on the relevance of time post-injury is reiterated here. Full article
(This article belongs to the Special Issue New Advances in Epigenetics and Epigenomics)
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14 pages, 1483 KiB  
Review
Additional Sex Combs-like Family Associated with Epigenetic Regulation
by Nackhyoung Kim, Sukyoung Byun and Soo-Jong Um
Int. J. Mol. Sci. 2024, 25(10), 5119; https://doi.org/10.3390/ijms25105119 - 8 May 2024
Cited by 1 | Viewed by 1252
Abstract
The additional sex combs-like (ASXL) family, a mammalian homolog of the additional sex combs (Asx) of Drosophila, has been implicated in transcriptional regulation via chromatin modifications. Abnormal expression of ASXL family genes leads to myelodysplastic syndromes and various types of [...] Read more.
The additional sex combs-like (ASXL) family, a mammalian homolog of the additional sex combs (Asx) of Drosophila, has been implicated in transcriptional regulation via chromatin modifications. Abnormal expression of ASXL family genes leads to myelodysplastic syndromes and various types of leukemia. De novo mutation of these genes also causes developmental disorders. Genes in this family and their neighbor genes are evolutionary conserved in humans and mice. This review provides a comprehensive summary of epigenetic regulations associated with ASXL family genes. Their expression is commonly regulated by DNA methylation at CpG islands preceding transcription starting sites. Their proteins primarily engage in histone tail modifications through interactions with chromatin regulators (PRC2, TrxG, PR-DUB, SRC1, HP1α, and BET proteins) and with transcription factors, including nuclear hormone receptors (RAR, PPAR, ER, and LXR). Histone modifications associated with these factors include histone H3K9 acetylation and methylation, H3K4 methylation, H3K27 methylation, and H2AK119 deubiquitination. Recently, non-coding RNAs have been identified following mutations in the ASXL1 or ASXL3 gene, along with circular ASXLs and microRNAs that regulate ASXL1 expression. The diverse epigenetic regulations linked to ASXL family genes collectively contribute to tumor suppression and developmental processes. Our understanding of ASXL-regulated epigenetics may provide insights into the development of therapeutic epigenetic drugs. Full article
(This article belongs to the Special Issue New Advances in Epigenetics and Epigenomics)
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