Special Issue "DNA Methylation"
A special issue of Biology (ISSN 2079-7737).
Deadline for manuscript submissions: closed (30 April 2014)
Prof. Dr. Melanie Ehrlich
Hayward Human Genetics Center, Tulane Cancer Center, and the Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, USA
Interests: DNA methylation; chromatin epigenetics; regulation of skeletal muscle development; cancer epigenetics
Improvements in methodology for analyzing animal and plant DNA methylation, especially in genome-wide studies (methylome analysis), are bringing new insights into the functions of modification of genomic cytosine residues(5-methylcytosine, 5mC, and the much less plentiful 5-hydroxymethylcytosine, 5hmC). DNA methylation profiles coupled with data on gene expression, histone modification, transcription factor binding, open chromatin and the results of experimental manipulation of DNA methylation are greatly advancing our understanding of the roles of genomic 5mC in normal development, physiology, and disease. These studies are revealing increasingly varied and context-dependent consequences of increases and decreases in DNA methylation on gene expression that are only beginning to be generally recognized.
Recent investigations of mammalian genomic 5hmC, which is generated from 5mC residues, indicate distinct functional and chromatin structural associations from those of 5mC. The role of genomic 5hmC as an intermediate in the conversion of 5mC to unmodified C residues and the biological significance of the stable fraction of this DNA base in differentiation, cellular function (especially in the nervous system), and pathology are being intensively investigated. Tissue-specific differences and cancer-associated reductions in genomic 5hmC content suggest not only its importance in vivo, but also reaffirm that of the parent 5mC DNA residue. For this special issue we invite research articles on any of the frontiers of DNA methylation research.
Prof. Dr. Melanie Ehrlich
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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed Open Access quarterly journal published by MDPI.
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- DNA methylation
- methylome epigenetics
- chromatin modification
- regulation of gene expression
Biology 2014, 3(3), 498-513; doi:10.3390/biology3030498
Received: 26 May 2014; in revised form: 8 August 2014 / Accepted: 12 August 2014 / Published: 21 August 2014| PDF Full-text (149 KB) | HTML Full-text | XML Full-text
Review: Control of Glycosylation-Related Genes by DNA Methylation: the Intriguing Case of the B3GALT5 Gene and Its Distinct Promoters
Biology 2014, 3(3), 484-497; doi:10.3390/biology3030484
Received: 28 April 2014; in revised form: 22 July 2014 / Accepted: 25 July 2014 / Published: 4 August 2014| PDF Full-text (799 KB) | HTML Full-text | XML Full-text
Biology 2014, 3(2), 426-451; doi:10.3390/biology3020426
Received: 18 April 2014; in revised form: 21 May 2014 / Accepted: 21 May 2014 / Published: 19 June 2014| PDF Full-text (370 KB) | HTML Full-text | XML Full-text | Supplementary Files
Biology 2014, 3(2), 403-425; doi:10.3390/biology3020403
Received: 14 May 2014; in revised form: 28 May 2014 / Accepted: 31 May 2014 / Published: 18 June 2014| PDF Full-text (253 KB) | HTML Full-text | XML Full-text
Biology 2014, 3(2), 243-254; doi:10.3390/biology3020243
Received: 17 February 2014; in revised form: 18 March 2014 / Accepted: 20 March 2014 / Published: 26 March 2014| PDF Full-text (219 KB) | HTML Full-text | XML Full-text
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Type of Paper: Review
Title: Dnmt3b prefers germline genes and centromeric regions: implications for diseases
Authors: Emma Walton, Guillaume Velasco and Claire Francastel
Affiliations: UMR7216 Epigenetics and Cell Fate, CNRS, Université Paris 7, Paris, France; E-Mail: email@example.com
Abstract: Correct establishment and maintenance of DNA methylation patterns are critical for mammalian development and control of normal cell growth and differentiation. DNA methylation has profound effects on the mammalian genome, including transcriptional repression, chromatin structure modulation, X chromosome inactivation, genomic imprinting, and the suppression of the detrimental effects of repetitive and parasitic DNA sequences on genome integrity. Consistent with its essential role in normal cells and predominance at repetitive genomic regions, changes to patterns of DNA methylation are commonly observed in diseases with chromosomal and genomic instabilities. In this context, expression or catalytic activity of the enzymes that catalyze the modification, the DNA methyltransferases (DNMT), appear to be particularly affected. DNMT3B, involved in de novo methylation, is of particular interest not only because of its important role in development, but also because of its strong links to disease. Catalytically inactive variants have been associated with cancer risk and germline hypomorphic mutations with the ICF syndrome (Immunodeficiency Centromeric instability Facial anomalies). In these diseases, a global genomic hypomethylation affects repeated sequences around centromeric regions, the main hallmark of heterochromatin, in association with chromosome instability, impaired chromosome segregation and perturbed nuclear architecture. The review will focus on recent data on the activity of Dnmt3b and its variants, and the consequences of its deregulated activity on pathological DNA hypomethylation, illicit activation of germline-specific genes and accumulation of transcripts originating from repeated satellite sequences as original physiopathological biomarkers for these diseases. We will also question the potential functional impact of these deregulated protein-coding and non-coding transcription programs on perturbation of cellular and nuclear phenotypes.
Type of Paper: Review
Title: DNA methylation analysis: Methods
Author: Sergey Kurdyukov
Affiliation: Kolling Institute of Medical Research, University of Sydney, Sydney, Australia; E-Mail: firstname.lastname@example.org
Abstract: In the burgeoning field of epigenetics there are a number of methods for DNA methylation analysis. How one could find the right method to answers a specific biological question? The review is aiming to provide an algorithm for researchers that are new to the area. All modern techniques for DNA methylation analysis are scrutinized and ranked according to their robustness, high throughput capabilities and cost. Separate sections are dedicated to methods that are suitable for investigation of global methylation profiling and methylation status of specific genes of interest.
Type of Paper: Review
Title: DNA methylation, genome evolution and phenotypic divergence
Authors: Kei Fukuda and Kenji Ichiyanagi *
Affiliation: Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; E-Mail:
Abstract: Epigenetic regulation by DNA methylation plays important roles in gene regulation, transposon silencing, cell differentiation, ontogenesis, and pathogenesis in the mammalian system. The epigenome can be altered in response to environmental changes, leading to phenotypic changes, and the altered state of epigenome is in some cases inherited across generations. Recent comparative studies on DNA methylation between different species and within population of a species have revealed the importance of DNA methylation in phenotypic divergence and evolution. However, the molecular mechanisms that alter the DNA methylation pattern remains largely unknown. In this review, we summarize the current understanding on genome-epigenome interactions and discuss their implications in mammalian evolution and human diseases.
Type of Paper: Review
Title: DNA modifications: function and applications in normal and disease states
Authors: Vichithra R B Liyanage 1, Jessica Jarmasz 2, Marc R Del Bigio 3, Mojgan Rastegar 1 and James R Davie 1,*
1 Department of Biochemistry and Medical Genetics, University of Manitoba, Manitoba Institute of Cell Biology, Winnipeg, Manitoba, Canada; E-Mail: email@example.com
2 Department of Human Anatomy and Cell Science, University of Manitoba
3 Department of Pathology, University of Manitoba
Abstract: Epigenetics refers to a variety of processes that have heritable effects on gene expression programs without changes in DNA sequence. Key players in epigenetic control are chemical modifications to DNA, histone and non-histone chromosomal proteins which establish a complex regulatory network that controls genome function. Methylation of DNA at the 5th position of cytosine in CpG dinucleotides (5-methylcytosine, 5-mC), which is carried out by DNA methyltransferases, is commonly associated with gene silencing. However, high resolution mapping of DNA methylation has revealed that 5-mC is enriched in exonic nucleosomes and at intron-exon junctions, suggesting a role of DNA methylation in the relationship between elongation and RNA splicing. Recent studies have increased our knowledge of another modification of DNA, 5-hydroxymethylcytosine (5-hmC), which is a product of the TET proteins converting 5-mC to 5-hmC. In this review, we will highlight current studies on the role of 5-mC and 5-hmC in regulating gene expression. Further the role of these modifications in and detection of pathological states (type 2 diabetes, Rett syndrome, and Fetal alcohol spectrum disorders) will be discussed.
Last update: 9 December 2013