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Epigenomes
Special Issues
Histone Variants
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Histone Variants

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

Deadline for manuscript submissions: 30 April 2025 | Viewed by 4193

Special Issue Editor

Dr. Chunyuan Jin

E-Mail Website
Guest Editor
Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
Interests: environmental epigenetics; histone variant; chromatin; environmental carcinogenesis; heavy metal; aldehyde

Special Issue Information

Dear Colleagues,

Histone proteins wrap around DNA, forming nucleosomes that serve to package and organize DNA within the nucleus while controlling its accessibility.

In addition to the canonical histones, there are variant histones that possess distinct gene and mRNA structures, as well as unique amino acid sequences compared with their canonical counterparts. Unlike canonical histones, which are primarily expressed during the S phase and deposited onto chromatin through a replication-coupled mechanism, histone variants are expressed throughout the cell cycle and deposited at specific genomic locations via a replication-independent process, facilitated by variant-specific histone chaperones.

Replacing canonical histones with variant histones within a nucleosome imparts unique properties to the nucleosomes, influencing chromatin stability, dynamics, and organization. Histone variants have been shown to play pivotal roles in processes such as transcription, DNA replication and repair, chromosome segregation, and those related to development, aging, and diseases like cancer.

This Special Issue is focused on the latest advances in our understanding of various aspects related to histone variants. We welcome submissions of reviews, research articles, and method manuscripts that offer exceptional insights into the following topics:

  1. Histone variants, their chaperones, and deposition mechanisms.
  2. Post-translational modifications of histone variants.
  3. Histone variants in regulating nucleosome stability, structure, and function.
  4. Histone variants in genome integrity and epigenetic memory.
  5. Alterations in histone variants in response to environmental exposures.
  6. Histone variants in development, aging, and disease.

Dr. Chunyuan Jin
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

  • histone variant
  • epigenetics
  • chaperone
  • chromatin
  • nucleosome
  • assembly
  • post-translational modification
  • gene expression
  • replication-independent

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Published Papers (3 papers)

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19 pages, 11563 KiB  
Article
Epigenome Mapping in Quiescent Cells Reveals a Key Role for H3K4me3 in Regulation of RNA Polymerase II Activity
by Shengyuan Zeng and Karl Ekwall
Epigenomes 2024, 8(4), 39; https://doi.org/10.3390/epigenomes8040039 - 22 Oct 2024
Viewed by 904
Abstract
(1) Background: Quiescent cells are those that have stopped dividing and show strongly reduced levels of gene expression during dormancy. In response to appropriate signals, the cells can wake up and start growing again. Many histone modifications are regulated in quiescence, but their [...] Read more.
(1) Background: Quiescent cells are those that have stopped dividing and show strongly reduced levels of gene expression during dormancy. In response to appropriate signals, the cells can wake up and start growing again. Many histone modifications are regulated in quiescence, but their exact functions remain to be determined. (2) Methods: Here, we map the different histone modifications, H3K4me3, H3K9ac, H3K9me2, and H3K9me3, and the histone variant H2A.Z, comparing vegetative and quiescent fission yeast (S. pombe) cells. We also map histone H3 as a control and RNA polymerase II (phosphorylated at S2 and S5) to enable comparisons of their occupancies within genes. We use ChIP-seq methodology and several different bioinformatics tools. (3) Results: The histone modification mapping data show that H3K4me3 changes stand out as being the most significant. Changes in occupancy of histone variant H2A.Z were also significant, consistent with earlier studies. Regarding gene expression changes in quiescence, we found that changes in mRNA levels were associated with changes in occupancy of RNA polymerase II (S2 and S5). Analysis of quiescence genes showed that increased H3K4me3 levels and RNA polymerase II occupancy were super-significant in a small set of core quiescence genes that are continuously upregulated during dormancy. We demonstrate that several of these genes were require Set1C/COMPASS activity for their strong induction during quiescence. (4) Conclusions: Our results imply that regulation of gene expression in quiescent cells involves epigenome changes with a key role for H3K4me3 in regulation of RNA polymerase II activity, and that different gene activation mechanisms control early and core quiescence genes. Thus, our data give further insights into important epigenome changes in quiescence using fission yeast as an experimental model. Full article
(This article belongs to the Special Issue Histone Variants)
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13 pages, 3662 KiB  
Article
Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z
by Harry Jung, Vladyslava Sokolova, Gahyun Lee, Victoria Rose Stevens and Dongyan Tan
Epigenomes 2024, 8(2), 21; https://doi.org/10.3390/epigenomes8020021 - 27 May 2024
Cited by 1 | Viewed by 1860
Abstract
Variant H3.3, along with H2A.Z, is notably enriched at promoter regions and is commonly associated with transcriptional activation. However, the specific molecular mechanisms through which H3.3 influences chromatin dynamics at transcription start sites, and its role in gene regulation, remain elusive. Using a [...] Read more.
Variant H3.3, along with H2A.Z, is notably enriched at promoter regions and is commonly associated with transcriptional activation. However, the specific molecular mechanisms through which H3.3 influences chromatin dynamics at transcription start sites, and its role in gene regulation, remain elusive. Using a combination of biochemistry and cryo-electron microscopy (cryo-EM), we show that the inclusion of H3.3 alone does not induce discernible changes in nucleosome DNA dynamics. Conversely, the presence of both H3.3 and H2A.Z enhances DNA’s flexibility similarly to H2A.Z alone. Interestingly, our findings suggest that the presence of H3.3 in the H2A.Z nucleosome provides slightly increased protection to DNA at internal sites within the nucleosome. These results imply that while H2A.Z at active promoters promotes the formation of more accessible nucleosomes with increased DNA accessibility to facilitate transcription, the simultaneous presence of H3.3 offers an additional mechanism to fine-tune nucleosome accessibility and the chromatin environment. Full article
(This article belongs to the Special Issue Histone Variants)
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Other

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8 pages, 694 KiB  
Opinion
Histone Modification Pathways Suppressing Cryptic Transcription
by Hong-Yeoul Ryu
Epigenomes 2024, 8(4), 42; https://doi.org/10.3390/epigenomes8040042 - 12 Nov 2024
Viewed by 628
Abstract
Cryptic transcription refers to the unintended expression of non-canonical sites within the genome, producing aberrant RNA and proteins that may disrupt cellular functions. In this opinion piece, I will explore the role of histone modifications in modulating cryptic transcription and its implications for [...] Read more.
Cryptic transcription refers to the unintended expression of non-canonical sites within the genome, producing aberrant RNA and proteins that may disrupt cellular functions. In this opinion piece, I will explore the role of histone modifications in modulating cryptic transcription and its implications for gene expression and cellular integrity, particularly with a focus on H3K36 and H3K4 methylation marks. H3K36 tri-methylation plays a crucial role in maintaining chromatin integrity by facilitating the recruitment of the Rpd3S histone deacetylase (HDAC) complex, which helps restore closed chromatin states following transcription and prevents cryptic initiation within gene bodies. In parallel, crosstalk between H3K4 di-methylation and histone ubiquitylation and sumoylation is critical for recruiting the Set3 HDAC complex, which maintains low histone acetylation levels in gene bodies and further suppresses cryptic transcription. Therefore, by elucidating these regulatory mechanisms, this opinion highlights the intricate interplay of histone modifications in preserving transcriptional fidelity and suggests potential pathways for future research to develop novel therapies for age-related disorders and other diseases associated with dysregulated gene expression. Full article
(This article belongs to the Special Issue Histone Variants)
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