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Epigenetic Control of Chromatin Organization and Plasticity
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Epigenetic Control of Chromatin Organization and Plasticity

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (20 November 2021) | Viewed by 16266

Special Issue Editor

Dr. Vincenzo Cavalieri

E-Mail Website
Guest Editor
Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
Interests: epigenetics; gene regulation; chromatin; embryogenesis; zebrafish

Special Issue Information

Dear Colleagues,

The genomic information of each eukaryotic cell is packaged within the nucleus in the form of chromatin, a polymeric complex composed primarily of DNA and histone proteins, but also comprising noncoding RNA and a multiplicity of structural nonhistone proteins. Nucleosomes act as fundamental units of chromatin packaging and play pivotal roles in the coordination between chromatin architecture and functions by means of epigenetic mechanisms. These include covalent modifications of DNA and histones, exchange of specialized histone variants into existing nucleosomes, nucleosome positioning and density, three-dimensional chromatin organization, noncoding RNAs, and transcriptional regulatory networks. The harmonious combination of all these epigenetic mechanisms dynamically controls the degree of chromatin condensation and determines spatiotemporal patterns of gene transcription for a given cell/organism, thus contributing to an extensive range of biological processes. This Special Issue aims to cover recent progress in this exciting field of research.

Prof. Dr. Vincenzo Cavalieri
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. Genes 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 2600 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

  • Chromatin dynamics
  • Chromatin architecture
  • Nucleosome
  • Epigenetics
  • DNA methylation
  • Histone post-translational modifications
  • Histone-modifying activities
  • Histone variants
  • Noncoding RNA
  • Regulatory networks

Published Papers (4 papers)

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Review

20 pages, 1452 KiB  
Review
Roles of the Core Components of the Mammalian miRISC in Chromatin Biology
by Gaspare La Rocca and Vincenzo Cavalieri
Genes 2022, 13(3), 414; https://doi.org/10.3390/genes13030414 - 24 Feb 2022
Cited by 4 | Viewed by 2401
Abstract
The Argonaute (AGO) and the Trinucleotide Repeat Containing 6 (TNRC6) family proteins are the core components of the mammalian microRNA-induced silencing complex (miRISC), the machinery that mediates microRNA function in the cytoplasm. The cytoplasmic miRISC-mediated post-transcriptional gene repression has been established as the [...] Read more.
The Argonaute (AGO) and the Trinucleotide Repeat Containing 6 (TNRC6) family proteins are the core components of the mammalian microRNA-induced silencing complex (miRISC), the machinery that mediates microRNA function in the cytoplasm. The cytoplasmic miRISC-mediated post-transcriptional gene repression has been established as the canonical mechanism through which AGO and TNRC6 proteins operate. However, growing evidence points towards an additional mechanism through which AGO and TNRC6 regulate gene expression in the nucleus. While several mechanisms through which miRISC components function in the nucleus have been described, in this review we aim to summarize the major findings that have shed light on the role of AGO and TNRC6 in mammalian chromatin biology and on the implications these novel mechanisms may have in our understanding of regulating gene expression. Full article
(This article belongs to the Special Issue Epigenetic Control of Chromatin Organization and Plasticity)
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22 pages, 825 KiB  
Review
The Expanding Constellation of Histone Post-Translational Modifications in the Epigenetic Landscape
by Vincenzo Cavalieri
Genes 2021, 12(10), 1596; https://doi.org/10.3390/genes12101596 - 10 Oct 2021
Cited by 43 | Viewed by 5027
Abstract
The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of [...] Read more.
The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of epigenetic mechanisms. Notably, such an epigenetic machinery involves an overwhelming number of post-translational modifications at multiple residues of core and linker histones. This review aims to comprehensively describe old and recent evidence in this exciting field of research. In particular, histone post-translational modification establishing/removal mechanisms, their genomic locations and implication in nucleosome dynamics and chromatin-based processes, as well as their harmonious combination and interdependence will be discussed. Full article
(This article belongs to the Special Issue Epigenetic Control of Chromatin Organization and Plasticity)
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Figure 1

17 pages, 1082 KiB  
Review
Epigenetic Contribution and Genomic Imprinting Dlk1-Dio3 miRNAs in Systemic Lupus Erythematosus
by Rujuan Dai, Zhuang Wang and S. Ansar Ahmed
Genes 2021, 12(5), 680; https://doi.org/10.3390/genes12050680 - 1 May 2021
Cited by 10 | Viewed by 3079
Abstract
Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease that afflicts multiple organs, especially kidneys and joints. In addition to genetic predisposition, it is now evident that DNA methylation and microRNAs (miRNAs), the two major epigenetic modifications, are critically involved in the pathogenesis [...] Read more.
Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease that afflicts multiple organs, especially kidneys and joints. In addition to genetic predisposition, it is now evident that DNA methylation and microRNAs (miRNAs), the two major epigenetic modifications, are critically involved in the pathogenesis of SLE. DNA methylation regulates promoter accessibility and gene expression at the transcriptional level by adding a methyl group to 5′ cytosine within a CpG dinucleotide. Extensive evidence now supports the importance of DNA hypomethylation in SLE etiology. miRNAs are small, non-protein coding RNAs that play a critical role in the regulation of genome expression. Various studies have identified the signature lupus-related miRNAs and their functional contribution to lupus incidence and progression. In this review, the mutual interaction between DNA methylation and miRNAs regulation in SLE is discussed. Some lupus-associated miRNAs regulate DNA methylation status by targeting the DNA methylation enzymes or methylation pathway-related proteins. On the other hand, DNA hyper- and hypo-methylation are linked with dysregulated miRNAs expression in lupus. Further, we specifically discuss the genetic imprinting Dlk1-Dio3 miRNAs that are subjected to DNA methylation regulation and are dysregulated in several autoimmune diseases, including SLE. Full article
(This article belongs to the Special Issue Epigenetic Control of Chromatin Organization and Plasticity)
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41 pages, 3092 KiB  
Review
RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases
by Amber Willbanks, Shaun Wood and Jason X. Cheng
Genes 2021, 12(5), 627; https://doi.org/10.3390/genes12050627 - 22 Apr 2021
Cited by 15 | Viewed by 4811
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating [...] Read more.
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases. Full article
(This article belongs to the Special Issue Epigenetic Control of Chromatin Organization and Plasticity)
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