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Epigenomes
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Epigenetics of the Nervous System 2.0
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Epigenetics of the Nervous System 2.0

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

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 14041

Special Issue Editors

Prof. Dr. Che-Kun James Shen

E-Mail Website
Guest Editor
1. The PhD Program for Neural Regenerative Medicine, Taipei Medical University, Taipei 115, Taiwan
2. Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
Interests: gene regulation; chromatin; DNA methylation; neurofunction; transcription
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Guoping Fan

E-Mail Website
Guest Editor
Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Gonda BLDG Rm. 6554, P.O. Box 957088, Los Angeles, CA 90095-7088, USA
Interests: epigenetics; gene expression; DNA methylation; neural stem cell differentiation; adult brain function; somatic cell reprogramming
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the last few years, epigenetic modifications in the nervous system have proven to be fundamental for the correct development and function of the brain. It is well known that DNA methylation is associated with learning as well as with the development of several neurological disorders including neurodegeneration.

This Special Issue will be focused on the epigenetic changes that take place in the nervous system, from adolescent development through adulthood. In addition to invited reviews, we welcome research and/or methods manuscripts of exceptional interest on the following topics:

  • Effect of epigenetic changes in neural stem cells
  • Epigenetics and neuropathology
  • Animal models for the study of the relationship between epigenetics and the nervous system
  • Human neural pathologies and epigenetics

Prof. Dr. Che-Kun James Shen
Prof. Dr. Guoping Fan
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.

Published Papers (3 papers)

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Research

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10 pages, 2440 KiB  
Article
Exploring DNA Methylation Diversity in the Honey Bee Brain by Ultra-Deep Amplicon Sequencing
by Robert Kucharski and Ryszard Maleszka
Epigenomes 2020, 4(2), 10; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4020010 - 25 Jun 2020
Cited by 11 | Viewed by 3667
Abstract
Understanding methylation dynamics in organs or tissues containing many different cell types is a challenging task that cannot be efficiently addressed by the low-depth bisulphite sequencing of DNA extracted from such sources. Here we explored the feasibility of ultra-deep bisulphite sequencing of long [...] Read more.
Understanding methylation dynamics in organs or tissues containing many different cell types is a challenging task that cannot be efficiently addressed by the low-depth bisulphite sequencing of DNA extracted from such sources. Here we explored the feasibility of ultra-deep bisulphite sequencing of long amplicons to reveal the brain methylation patterns in three selected honey bee genes analysed across five distinct conditions on the Illumina MiSeq platform. By combing 15 libraries in one run we achieved a very high sequencing depth of 240,000–340,000 reads per amplicon, suggesting that most of the cell types in the honey bee brain, containing approximately 1 million neurons, are represented in this dataset. We found a small number of gene-specific patterns for each condition in individuals of different ages and performing distinct tasks with 80–90% of those were represented by no more than a dozen patterns. One possibility is that such a small number of frequent patterns is the result of differentially methylated epialleles, whereas the rare and less frequent patterns reflect activity-dependent modifications. The condition-specific methylation differences within each gene appear to be position-dependent with some CpGs showing significant changes and others remaining stable in a methylated or non-methylated state. Interestingly, no significant loss of methylation was detected in very old individuals. Our findings imply that these diverse patterns represent a special challenge in the analyses of DNA methylation in complex tissues and organs that cannot be investigated by low-depth genome-wide bisulphite sequencing. We conclude that ultra-deep sequencing of gene-specific amplicons combined with genotyping of differentially methylated epialleles is an effective way to facilitate more advanced neuro-epigenomic studies in honey bees and other insects. Full article
(This article belongs to the Special Issue Epigenetics of the Nervous System 2.0)
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Review

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15 pages, 271 KiB  
Review
Epigenomic Remodeling in Huntington’s Disease—Master or Servant?
by Geraldine Zimmer-Bensch
Epigenomes 2020, 4(3), 15; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4030015 - 31 Jul 2020
Cited by 5 | Viewed by 4295
Abstract
In light of our aging population, neurodegenerative disorders are becoming a tremendous challenge, that modern societies have to face. They represent incurable, progressive conditions with diverse and complex pathological features, followed by catastrophic occurrences of massive neuronal loss at the later stages of [...] Read more.
In light of our aging population, neurodegenerative disorders are becoming a tremendous challenge, that modern societies have to face. They represent incurable, progressive conditions with diverse and complex pathological features, followed by catastrophic occurrences of massive neuronal loss at the later stages of the diseases. Some of these disorders, like Huntington’s disease (HD), rely on defined genetic factors. HD, as an incurable, fatal hereditary neurodegenerative disorder characterized by its mid-life onset, is caused by the expansion of CAG trinucleotide repeats coding for glutamine (Q) in exon 1 of the huntingtin gene. Apart from the genetic defect, environmental factors are thought to influence the risk, onset and progression of HD. As epigenetic mechanisms are known to readily respond to environmental stimuli, they are proposed to play a key role in HD pathogenesis. Indeed, dynamic epigenomic remodeling is observed in HD patients and in brains of HD animal models. Epigenetic signatures, such as DNA methylation, histone variants and modifications, are known to influence gene expression and to orchestrate various aspects of neuronal physiology. Hence, deciphering their implication in HD pathogenesis might open up new paths for novel therapeutic concepts, which are discussed in this review. Full article
(This article belongs to the Special Issue Epigenetics of the Nervous System 2.0)
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Other

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7 pages, 818 KiB  
Brief Report
Global DNA Methylation in the Limbic System of Cattle
by Bonnie Cantrell, Hannah Lachance, Brenda Murdoch, Julia Sjoquist, Richard Funston, Robert Weaber and Stephanie McKay
Epigenomes 2019, 3(2), 8; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes3020008 - 05 May 2019
Cited by 7 | Viewed by 5396
Abstract
To elucidate the extent to which DNA methylation varies across multiple tissues in the brain and between animals, we have quantified global DNA methylation in tissues comprising the limbic system for six Red Angus x Simmental steers. Global DNA methylation was measured in [...] Read more.
To elucidate the extent to which DNA methylation varies across multiple tissues in the brain and between animals, we have quantified global DNA methylation in tissues comprising the limbic system for six Red Angus x Simmental steers. Global DNA methylation was measured in nine regions of the bovine brain: amygdala, the bed nucleus of the stria terminalis, cingulate gyrus, dorsal raphe, hippocampus, hypothalamus, nucleus accumbens, periaqueductal gray and prefrontal cortex. DNA methylation varies among animals for each tissue type and varies among tissue types for each animal. The highest amounts of DNA methylation were found in the amygdala, cingulate gyrus and dorsal raphe, while the bed nucleus of the stria terminalis, nucleus accumbens and periaqueductal gray had the lowest amounts of DNA methylation. A heatmap sorted by k-means clustering was generated to graphically display percent DNA methylation in relation to tissue type and animal number. This is the first study to report measures of DNA methylation in the limbic system of the bovine brain and can be used to inform the cattle genomics community of expected variation in cattle brain methylation. Full article
(This article belongs to the Special Issue Epigenetics of the Nervous System 2.0)
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