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Epigenomes
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Chromatin Unlimited
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Chromatin Unlimited

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 19961

Special Issue Editor

Prof. Dr. Yasushi Hiraoka

E-Mail Website
Guest Editor
Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
Interests: chromosome; nuclear envelope; nuclear structures; mitosis; meiosis

Special Issue Information

Dear Colleagues,

Chromatin is a fundamental and highly conserved structure that carries the genetic and epigenetic information in eukaryotic cells. When claiming evolutionary conservation, we often say “yeasts to humans.” However, yeasts and humans belong to the same taxonomic supergroup, Opisthokonta, within a narrow range of eukaryotes. Several organisms are known to have evolved non-canonical forms of chromatin, such as in dinoflagellates or ciliated protozoans. Mammalian sperm chromatin and erythrocyte chromatin are other examples of non-canonical chromatin.

In this Special Issue “Chromatin Unlimited”, we aim to highlight chromatin in a wider range of eukaryotes. A deeper understanding of the non-canonical forms of chromatin will paradoxically shed a light on the essentials of the most common canonical ones. We welcome reviews, mini-reviews, original research articles, and short communications that put into perspective or advance our understanding of both canonical and non-canonical chromatin. We also welcome a consideration of the relevant studies proposing hypothetical models or new technologies for understanding chromatin.

Prof. Dr. Yasushi Hiraoka
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. 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.

Keywords

  • canonical and non-canonical chromatin
  • nucleosome
  • histone
  • SMC protein
  • evolution
  • phylogeny
  • comparative genomics
  • non-model organisms

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Published Papers (5 papers)

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Editorial

Jump to: Review

2 pages, 184 KiB  
Editorial
Chromatin Unlimited: An Evolutionary View of Chromatin
by Yasushi Hiraoka
Epigenomes 2022, 6(1), 2; https://doi.org/10.3390/epigenomes6010002 - 2 Jan 2022
Viewed by 3131
Abstract
Chromatin is a fundamental and highly conserved structure that carries genetic and epigenetic information in eukaryotic cells [...] Full article
(This article belongs to the Special Issue Chromatin Unlimited)

Review

Jump to: Editorial

11 pages, 12119 KiB  
Review
Centromere Chromatin Dynamics at a Glance
by Shivangi Shukla and Ashutosh Kumar
Epigenomes 2022, 6(4), 39; https://doi.org/10.3390/epigenomes6040039 - 3 Nov 2022
Cited by 2 | Viewed by 2978
Abstract
The centromere is a specialized DNA locus that ensures the faithful segregation of chromosomes during cell division. It does so by directing the assembly of an essential proteinaceous structure called the kinetochore. The centromere identity is primarily epigenetically defined by a nucleosome containing [...] Read more.
The centromere is a specialized DNA locus that ensures the faithful segregation of chromosomes during cell division. It does so by directing the assembly of an essential proteinaceous structure called the kinetochore. The centromere identity is primarily epigenetically defined by a nucleosome containing an H3 variant called CENP-A as well as by the interplay of several factors such as differential chromatin organization driven by CENP-A and H2A.Z, centromere-associated proteins, and post-translational modifications. At the centromere, CENP-A is not just a driving force for kinetochore assembly but also modifies the structural and dynamic properties of the centromeric chromatin, resulting in a distinctive chromatin organization. An additional level of regulation of the centromeric chromatin conformation is provided by post-translational modifications of the histones in the CENP-A nucleosomes. Further, H2A.Z is present in the regions flanking the centromere for heterochromatinization. In this review, we focus on the above-mentioned factors to describe how they contribute to the organization of the centromeric chromatin: CENP-A at the core centromere, post-translational modifications that decorate CENP-A, and the variant H2A.Z. Full article
(This article belongs to the Special Issue Chromatin Unlimited)
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11 pages, 1145 KiB  
Review
R-Loop Formation in Meiosis: Roles in Meiotic Transcription-Associated DNA Damage
by Yasuhiro Fujiwara, Mary Ann Handel and Yuki Okada
Epigenomes 2022, 6(3), 26; https://doi.org/10.3390/epigenomes6030026 - 24 Aug 2022
Cited by 4 | Viewed by 4156
Abstract
Meiosis is specialized cell division during gametogenesis that produces genetically unique gametes via homologous recombination. Meiotic homologous recombination entails repairing programmed 200–300 DNA double-strand breaks generated during the early prophase. To avoid interference between meiotic gene transcription and homologous recombination, mammalian meiosis is [...] Read more.
Meiosis is specialized cell division during gametogenesis that produces genetically unique gametes via homologous recombination. Meiotic homologous recombination entails repairing programmed 200–300 DNA double-strand breaks generated during the early prophase. To avoid interference between meiotic gene transcription and homologous recombination, mammalian meiosis is thought to employ a strategy of exclusively transcribing meiotic or post-meiotic genes before their use. Recent studies have shown that R-loops, three-stranded DNA/RNA hybrid nucleotide structures formed during transcription, play a crucial role in transcription and genome integrity. Although our knowledge about the function of R-loops during meiosis is limited, recent findings in mouse models have suggested that they play crucial roles in meiosis. Given that defective formation of an R-loop can cause abnormal transcription and transcription-coupled DNA damage, the precise regulatory network of R-loops may be essential in vivo for the faithful progression of mammalian meiosis and gametogenesis. Full article
(This article belongs to the Special Issue Chromatin Unlimited)
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16 pages, 2868 KiB  
Review
Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses
by Shoko Sato, Mariko Dacher and Hitoshi Kurumizaka
Epigenomes 2022, 6(3), 22; https://doi.org/10.3390/epigenomes6030022 - 2 Aug 2022
Cited by 3 | Viewed by 4529
Abstract
In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been [...] Read more.
In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been limited to evolutionarily related organisms. The amino acid sequences of histone proteins are highly conserved from humans to yeasts, but are divergent in the deeply branching protozoan groups, including human parasites that are directly related to human health. Certain large DNA viruses, as well as archaeal organisms, contain distant homologs of eukaryotic histone proteins. The divergent sequences give rise to unique and distinct nucleosome architectures, although the fundamental principles of histone folding and DNA contact are highly conserved. In this article, we review the structures and biophysical properties of nucleosomes containing histones from the human parasites Giardia lamblia and Leishmania major, and histone-like proteins from the Marseilleviridae amoeba virus family. The presented data confirm the sharing of the overall DNA compaction system among evolutionally distant species and clarify the deviations from the species-specific nature of the nucleosome. Full article
(This article belongs to the Special Issue Chromatin Unlimited)
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13 pages, 2498 KiB  
Review
Making Mitotic Chromosomes in a Test Tube
by Keishi Shintomi
Epigenomes 2022, 6(3), 20; https://doi.org/10.3390/epigenomes6030020 - 20 Jul 2022
Cited by 2 | Viewed by 3538
Abstract
Mitotic chromosome assembly is an essential preparatory step for accurate transmission of the genome during cell division. During the past decades, biochemical approaches have uncovered the molecular basis of mitotic chromosomes. For example, by using cell-free assays of frog egg extracts, the condensin [...] Read more.
Mitotic chromosome assembly is an essential preparatory step for accurate transmission of the genome during cell division. During the past decades, biochemical approaches have uncovered the molecular basis of mitotic chromosomes. For example, by using cell-free assays of frog egg extracts, the condensin I complex central for the chromosome assembly process was first identified, and its functions have been intensively studied. A list of chromosome-associated proteins has been almost completed, and it is now possible to reconstitute structures resembling mitotic chromosomes with a limited number of purified factors. In this review, I introduce how far we have come in understanding the mechanism of chromosome assembly using cell-free assays and reconstitution assays, and I discuss their potential applications to solve open questions. Full article
(This article belongs to the Special Issue Chromatin Unlimited)
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