Special Issue "Epigenome, Epitranscriptome and Single Cell Analysis in Cell Fate Choice"

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

Deadline for manuscript submissions: closed (31 December 2019).

Special Issue Editors

Dr. Luciano Di Croce
E-Mail Website
Guest Editor
Center for Genomic Regulation, Barcelona, Spain
Interests: cancer epigenetics, Polycomb, chromatin remodeling, gene silencing, cellular differentiation, RNA modifications
Special Issues and Collections in MDPI journals
Dr. Maria R. Matarazzo
E-Mail Website
Guest Editor
Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
Interests: epigenetics; regulation of gene expression; chromatin; methylation; epigenomics; chromatin structure
Dr. Annalisa Fico
E-Mail Website
Guest Editor
Institute of Genetics and Biophysics Adriano Buzzati Traverso, 80131 Naples, Italy
Interests: stem cells; pluripotency/differentiation; neuroscience; neurodegenerative disease; cell metabolism; cell signaling; non-coding RNA
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

The epigenome refers to the complete DNA methylation, histone modification, nucleosome occupancy, as well as coding and non-coding RNA expression in different cell types. These modifications can result in changes to the structure of chromatin and changes to the function of the genome.The importance of analyzing these modifications at the single cell level is rapidly emerging as a revolutionary reserch area. Similarly, understanding the function and mechanisms of the dynamic RNA modifications, which are termed “RNA epigenetics”, represents a new challenge at the frontier between different disciplines, such as biochemistry, epigenetics, and cutting-edge technology. Reversible RNA modifications add a new dimension to the developing picture of post-transcriptional regulation of gene expression. This new dimension awaits integration with transcriptional regulation (i.e., DNA modifications), to decipher the multi-layered information that controls a plethora of biological functions. The epitranscriptome includes all the biochemical modifications of the RNA (the transcriptome) within a cell. Thus, in the era of advanced technologies, the exciting next step is to move from mapping nucleotide modifications to understanding how they contribute to biological processes.

In this Special Issue, we will consider reviews, research, or method manuscripts of exceptional interest on the following topics:

-Dynamic DNA and RNA modifications;

-Decoding the function of DNA and RNA modifications;

-DNA and RNA epigenetics in cell and development;

-Epigenomes and epitranscriptomes;

-Single cell analysis

Dr. Luciano Di Croce
Dr. Maria R. Matarazzo
Dr. Annalisa Fico
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 papers will be 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 1400 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
  • RNA modification
  • histone modification
  • N6-methyladenosine (m6A) 
  • epitranscriptome 
  • transcriptome 
  • epigenetics

Published Papers (5 papers)

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Editorial

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Open AccessEditorial
Interplay between DNA and RNA Modifications: A Constantly Evolving Process
Epigenomes 2020, 4(4), 26; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4040026 - 23 Nov 2020
Viewed by 795
Abstract
The epigenome refers to the entirety of DNA methylations, histone modifications, nucleosome occupancy, and coding and non-coding RNAs (and their modifications) in different cell types [...] Full article

Review

Jump to: Editorial

Open AccessReview
Anticodon Wobble Uridine Modification by Elongator at the Crossroad of Cell Signaling, Differentiation, and Diseases
Epigenomes 2020, 4(2), 7; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4020007 - 12 May 2020
Cited by 3 | Viewed by 1055
Abstract
First identified 20 years ago as an RNA polymerase II-associated putative histone acetyltransferase, the conserved Elongator complex has since been recognized as the central player of a complex, regulated, and biologically relevant epitranscriptomic pathway targeting the wobble uridine of some tRNAs. Numerous studies [...] Read more.
First identified 20 years ago as an RNA polymerase II-associated putative histone acetyltransferase, the conserved Elongator complex has since been recognized as the central player of a complex, regulated, and biologically relevant epitranscriptomic pathway targeting the wobble uridine of some tRNAs. Numerous studies have contributed to three emerging concepts resulting from anticodon modification by Elongator: the codon-specific control of translation, the ability of reprogramming translation in various physiological or pathological contexts, and the maintenance of proteome integrity by counteracting protein aggregation. These three aspects of tRNA modification by Elongator constitute a new layer of regulation that fundamentally contributes to gene expression and are now recognized as being critically involved in various human diseases. Full article
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Open AccessReview
Role of m6A in Embryonic Stem Cell Differentiation and in Gametogenesis
Epigenomes 2020, 4(1), 5; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4010005 - 14 Mar 2020
Cited by 4 | Viewed by 1493
Abstract
The rising field of RNA modifications is stimulating massive research nowadays. m6A, the most abundant mRNA modification is highly conserved during evolution. Through the last decade, the essential components of this dynamic mRNA modification machinery were found and classified into writer, [...] Read more.
The rising field of RNA modifications is stimulating massive research nowadays. m6A, the most abundant mRNA modification is highly conserved during evolution. Through the last decade, the essential components of this dynamic mRNA modification machinery were found and classified into writer, eraser and reader proteins. m6A modification is now known to take part in diverse biological processes such as embryonic development, cell circadian rhythms and cancer stem cell proliferation. In addition, there is already firm evidence for the importance of m6A modification in stem cell differentiation and gametogenesis, both in males and females. This review attempts to summarize the important results of recent years studying the mechanism underlying stem cell differentiation and gametogenesis processes. Full article
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Open AccessReview
LncRNAs and PRC2: Coupled Partners in Embryonic Stem Cells
Epigenomes 2019, 3(3), 14; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes3030014 - 06 Aug 2019
Cited by 3 | Viewed by 1923
Abstract
The power of embryonic stem cells (ESCs) lies in their ability to self-renew and differentiate. Behind these two unique capabilities is a fine-tuned molecular network that shapes the genetic, epigenetic, and epitranscriptomic ESC plasticity. Although RNA has been shown to be functionally important [...] Read more.
The power of embryonic stem cells (ESCs) lies in their ability to self-renew and differentiate. Behind these two unique capabilities is a fine-tuned molecular network that shapes the genetic, epigenetic, and epitranscriptomic ESC plasticity. Although RNA has been shown to be functionally important in only a small minority of long non-coding RNA genes, a growing body of evidence has highlighted the pivotal and intricate role of lncRNAs in chromatin remodeling. Due to their multifaceted nature, lncRNAs interact with DNA, RNA, and proteins, and are emerging as new modulators of extensive gene expression programs through their participation in ESC-specific regulatory circuitries. Here, we review the tight cooperation between lncRNAs and Polycomb repressive complex 2 (PRC2), which is intimately involved in determining and maintaining the ESC epigenetic landscape. The lncRNA-PRC2 partnership is fundamental in securing the fully pluripotent state of ESCs, which must be primed to differentiate properly. We also reflect on the advantages brought to this field of research by the advent of single-cell analysis. Full article
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Open AccessReview
Metabolic–Epigenetic Axis in Pluripotent State Transitions
Epigenomes 2019, 3(3), 13; https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes3030013 - 31 Jul 2019
Cited by 3 | Viewed by 2688
Abstract
Cell state transition (CST) occurs during embryo development and in adult life in response to different stimuli and is associated with extensive epigenetic remodeling. Beyond growth factors and signaling pathways, increasing evidence point to a crucial role of metabolic signals in this process. [...] Read more.
Cell state transition (CST) occurs during embryo development and in adult life in response to different stimuli and is associated with extensive epigenetic remodeling. Beyond growth factors and signaling pathways, increasing evidence point to a crucial role of metabolic signals in this process. Indeed, since several epigenetic enzymes are sensitive to availability of specific metabolites, fluctuations in their levels may induce the epigenetic changes associated with CST. Here we analyze how fluctuations in metabolites availability influence DNA/chromatin modifications associated with pluripotent stem cell (PSC) transitions. We discuss current studies and focus on the effects of metabolites in the context of naïve to primed transition, PSC differentiation and reprogramming of somatic cells to induced pluripotent stem cells (iPSCs), analyzing their mechanism of action and the causal correlation between metabolites availability and epigenetic alteration. Full article
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