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Epigenomes
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X-Chromosome Inactivation
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X-Chromosome Inactivation

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

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 20024

Special Issue Editors

Dr. Vincent Pasque

E-Mail Website
Guest Editor
Department of Development and Regeneration, University of Leuven—KU Leuven, B3000 Leuven, Belgium
Interests: early mammalian development; X-inactivation
Dr. Bradley Philip Balaton

E-Mail Website
Guest Editor
Department of Development and Regeneration, University of Leuven—KU Leuven, B3000 Leuven, Belgium
Interests: X-chromosome inactivation

Special Issue Information

Dear Colleagues,

X-chromosome inactivation (XCI) provides a paradigm for studying the wide-scale chromatin gene-silencing activities and gene dosage compensation of chromosomes, in which one of the two X-chromosomes in female mammals is inactivated to achieve dosage compensation with XY males. Despite being discovered in the 1960s, the pace of discoveries in XCI has increased greatly in the past few decades due to the rise of mammalian pluripotent stem cell embryo models and high-throughput omics technologies. Mechanistic studies have made great advances in dissecting the proteins and chromatin regulators responsible for XCI, yet questions remain about the initiation and choice of which X-chromosome to inactivate, and how the active X-chromosome may be upregulated to balance expression with autosomes. Additionally, as more work is performed in this field beyond mice, key differences between species have emerged, and the functional conversation and divergence of gene dosage compensation mechanisms remains a question of outstanding interest. XCI is also being studied to reactivate healthy copies of silenced genes. The influence of escape from XCI on diseases including cancer and brain disorders is also of key interest. Recent advances in stem cell models, embryo culture, single cell omics, super-resolution microscopy, and genome and epigenome editing provide exciting new tools to address unanswered questions and more.

This Special Issue will be focused on the study of mammalian X-chromosome inactivation, both on its mechanisms and its implications on health and phenotypes. We welcome all articles (both reviews and original research).

Dr. Vincent Pasque
Dr. Bradley Philip Balaton
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.

Keywords

  • X-chromosome inactivation
  • epigenetics
  • dosage compensation
  • non-coding RNA
  • gene silencing
  • chromatin
  • developmental epigenetics

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Published Papers (5 papers)

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Research

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10 pages, 1876 KiB  
Article
Age-Dependent DNA Methylation Variability on the X-Chromosome in Male and Female Twins
by Qihua Tan, Hikmat Alo, Marianne Nygaard, Mette Sørensen, Alisa Saleh, Jonas Mengel-From and Kaare Christensen
Epigenomes 2024, 8(4), 43; https://doi.org/10.3390/epigenomes8040043 - 18 Nov 2024
Viewed by 1408
Abstract
We aimed to explore the age-dependent epigenetic variability on the X-chromosome with consideration of X-chromosome inactivation by applying a sex-stratified regression analysis to DNA methylation array data on X-linked CpGs in aging identical twins. We found 13 X-linked CpGs showing age-related significant increase [...] Read more.
We aimed to explore the age-dependent epigenetic variability on the X-chromosome with consideration of X-chromosome inactivation by applying a sex-stratified regression analysis to DNA methylation array data on X-linked CpGs in aging identical twins. We found 13 X-linked CpGs showing age-related significant increase in variability in males (FDR < 0.05) but none in females. In females, we found a significantly higher proportion of CpGs showing increased variability with age among nominally significant (p < 0.05) CpGs under inactivation, but not among CpGs escaping inactivation. Survival analysis showed a slight trend of correlation by directional change in the variable CpGs with mortality in males. Compared with females, the male X-chromosome can be more vulnerable to epigenetic instability during aging. Full article
(This article belongs to the Special Issue X-Chromosome Inactivation)
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Review

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20 pages, 2263 KiB  
Review
A Comparative Analysis of Mouse Imprinted and Random X-Chromosome Inactivation
by Rebecca M. Malcore and Sundeep Kalantry
Epigenomes 2024, 8(1), 8; https://doi.org/10.3390/epigenomes8010008 - 10 Feb 2024
Cited by 4 | Viewed by 3105
Abstract
The mammalian sexes are distinguished by the X and Y chromosomes. Whereas males harbor one X and one Y chromosome, females harbor two X chromosomes. To equalize X-linked gene expression between the sexes, therian mammals have evolved X-chromosome inactivation as a dosage compensation [...] Read more.
The mammalian sexes are distinguished by the X and Y chromosomes. Whereas males harbor one X and one Y chromosome, females harbor two X chromosomes. To equalize X-linked gene expression between the sexes, therian mammals have evolved X-chromosome inactivation as a dosage compensation mechanism. During X-inactivation, most genes on one of the two X chromosomes in females are transcriptionally silenced, thus equalizing X-linked gene expression between the sexes. Two forms of X-inactivation characterize eutherian mammals, imprinted and random. Imprinted X-inactivation is defined by the exclusive inactivation of the paternal X chromosome in all cells, whereas random X-inactivation results in the silencing of genes on either the paternal or maternal X chromosome in individual cells. Both forms of X-inactivation have been studied intensively in the mouse model system, which undergoes both imprinted and random X-inactivation early in embryonic development. Stable imprinted and random X-inactivation requires the induction of the Xist long non-coding RNA. Following its induction, Xist RNA recruits proteins and complexes that silence genes on the inactive-X. In this review, we present a current understanding of the mechanisms of Xist RNA induction, and, separately, the establishment and maintenance of gene silencing on the inactive-X by Xist RNA during imprinted and random X-inactivation. Full article
(This article belongs to the Special Issue X-Chromosome Inactivation)
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22 pages, 1006 KiB  
Review
Orchestrating Asymmetric Expression: Mechanisms behind Xist Regulation
by Samuel Jesus Luchsinger-Morcelle, Joost Gribnau and Hegias Mira-Bontenbal
Epigenomes 2024, 8(1), 6; https://doi.org/10.3390/epigenomes8010006 - 1 Feb 2024
Cited by 4 | Viewed by 3997
Abstract
Compensation for the gene dosage disequilibrium between sex chromosomes in mammals is achieved in female cells by repressing one of its X chromosomes through a process called X chromosome inactivation (XCI), exemplifying the control of gene expression by epigenetic mechanisms. A critical player [...] Read more.
Compensation for the gene dosage disequilibrium between sex chromosomes in mammals is achieved in female cells by repressing one of its X chromosomes through a process called X chromosome inactivation (XCI), exemplifying the control of gene expression by epigenetic mechanisms. A critical player in this mechanism is Xist, a long, non-coding RNA upregulated from a single X chromosome during early embryonic development in female cells. Over the past few decades, many factors involved at different levels in the regulation of Xist have been discovered. In this review, we hierarchically describe and analyze the different layers of Xist regulation operating concurrently and intricately interacting with each other to achieve asymmetric and monoallelic upregulation of Xist in murine female cells. We categorize these into five different classes: DNA elements, transcription factors, other regulatory proteins, long non-coding RNAs, and the chromatin and topological landscape surrounding Xist. Full article
(This article belongs to the Special Issue X-Chromosome Inactivation)
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24 pages, 1883 KiB  
Review
Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation
by Samantha B. Peeters, Bronwyn J. Posynick and Carolyn J. Brown
Epigenomes 2023, 7(4), 29; https://doi.org/10.3390/epigenomes7040029 - 23 Nov 2023
Cited by 13 | Viewed by 6102
Abstract
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be [...] Read more.
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be expressed from the otherwise inactive X chromosome—in some cases constitutively, while other genes are variable between individuals, tissues or cells. In this review we discuss the advantages and disadvantages of the approaches that have been used to identify escapees. The identity of escapees provides important clues to mechanisms underlying escape from XCI, an arena of study now moving from correlation to functional studies. As most escapees show greater expression in females, the not-so-inactive X chromosome is a substantial contributor to sex differences in humans, and we highlight some examples of such impact. Full article
(This article belongs to the Special Issue X-Chromosome Inactivation)
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Graphical abstract

22 pages, 2388 KiB  
Review
IndiSPENsable for X Chromosome Inactivation and Gene Silencing
by Corinne Kaufmann and Anton Wutz
Epigenomes 2023, 7(4), 28; https://doi.org/10.3390/epigenomes7040028 - 2 Nov 2023
Cited by 2 | Viewed by 3855
Abstract
For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN [...] Read more.
For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN had been studied for its role in gene regulation in the context of cell signaling, including the NOTCH or nuclear hormone receptor signaling pathways. More recently, SPEN has been identified as a major regulator of initiation of chromosome-wide gene silencing during X chromosome inactivation (XCI) in mammals, where its function remains to be fully understood. Dependent on the biological context, SPEN functions via mechanisms which include different domains. While some domains of SPEN are highly conserved in sequence and secondary structure, species-to-species differences exist that might lead to mechanistic differences. Initiation of XCI appears to be different between humans and mice, which raises additional questions about the extent of generalization of SPEN’s function in XCI. In this review, we dissect the mechanism of SPEN in XCI. We discuss its subregions and domains, focusing on its role as a major regulator. We further highlight species-related research, specifically of mouse and human SPEN, with the aim to reveal and clarify potential species-to-species differences in SPEN’s function. Full article
(This article belongs to the Special Issue X-Chromosome Inactivation)
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