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DNA methylation of the Xist gene. The horizontal line indicates the Xist promoter region. The open rectangle indicates the 5 portion of the exon 1. The hooked arrow denotes the transcription start site. The methylation-sensitive restriction enzyme sites so far tested are shown: C, HhaI (CfoI); M, MluI; Sn, SnaBI, Sa, SacII; H, HpaII. The methylation status of the methylation-sensitive restriction sites is shown. Open circles indicate lack of methylation; solid circles indicate complete methylation; shaded circles indicate mosaic methylation in that a particular site is methylated with a certain probability on each allele. It is hypothesized that the promoter and the 5 end of exon 1 are mosaically methylated in eggs. Xi, inactive X chromosome; Xa, active X chromosome. Data for somatic cells and extraembryonic tissues are from reference 123; data for ES cells are from references 123 and 146; and data for germ cells are from references 4, 123, 124a, 168, and 169.
Source publication
Dosage compensation for X-linked genes in mammals is accomplished by inactivating one of the two X chromosomes in females. X-chromosome inactivation (XCI) occurs during development, coupled with cell differentiation. In somatic cells, XCI is random, whereas in extraembryonic tissues, XCI is imprinted in that the paternally inherited X chromosome is...
Contexts in source publication
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... methylation of the Xist gene in somatic cells correlates with its activity; the active Xist allele on the inactive X chro- mosome is unmethylated, whereas the inactive Xist allele on the active X chromosome is methylated (58, 123) (see also Fig. 6). Further evidence for the role of DNA methylation in the control of Xist expression in somatic cells is shown by studies with DNA MTase-deficient mice; the normally silent, and methylated, Xist allele on the single, active X chromosome in the male is induced to be expressed in the DNA MTase- deficient mice ...
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... as in XX ES cells (125). In undifferentiated female (XX) ES cells, where Xist expression is very low, CpG sites in the promoter region and the 5 end of the body of the Xist gene are mosaically methyl- ated (146); i.e., any particular CpG site on each allele is meth- ylated with a certain probability in a population of molecules of the Xist gene (Fig. ...
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... Xist expression occurs only from the paternal allele (imprinted), and this correlates with preferential inacti- vation of the paternal X chromosome in these tissues (73) (see below). The active Xist allele on the inactive paternal X chro- mosome is unmethylated, whereas the inactive allele on the active maternal X chromosome is methylated (123) (Fig. ...
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... in the androgenetic embryos (74,84,85). It has been proposed that DNA methylation is involved in the regulation of imprinted expression in preimplantation embryos (4,168). The promoter region (168) and the 5 end of the first exon (4) are differentially methylated at certain CpG sites, which are hypomethylated in sperm and methylated in oocytes (Fig. 6). More importantly, the methylation of the maternal Xist allele survives the genome-wide demethylation occurring in preim- plantation development (4,117,168). This strongly suggests that the differential methylation in sperm and oocytes is a candidate gametic imprint for the repression of the maternal allele of Xist, leading to ...
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... the maternal allele of Xist, leading to preferential paternal allele expression in preimplantation embryos. Later experiments have suggested that methylation of the promoter region in oocytes is mosaic, as seen for undifferentiated ES cells (169), and recent investi- gations involving bisulfite genomic sequencing supported these findings (124a) (Fig. ...
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... promoter in a methylation-dependent and sequence-specific manner. This protein, identified in ES cell nuclear extracts, recognizes the GC-rich sequence 5-GC GCCGCGG-3 (nt 44 to 36 from the transcription start site) encompassing three CpG sites differentially methylated in sperm and oocytes [the HhaI (5-GCGC-3) and SacII (5-CC GCGG-3) sites in Fig. 6] and binds to this sequence only when it is methylated at at least one of the three CpG sites it contains (64). Moreover, this sequence is important for transcription in its unmethylated form (64). Therefore, it is hypothesized that this repressor protein is also present in preimplantation em- bryos and is responsible for imprinted ...
Citations
... Genomic imprinting is the expression of a gene as determined by its parental origin (Goto and Monk, 1998). This process may also contribute to allelic expression or inactivation (Autuoro et al., 2014). ...
Inherited retinal diseases (IRDs) are a group of heterogeneous conditions that cause progressive vision loss, typically due to monogenic mutations. Female carriers of X-linked IRDs have a single copy of the disease-causing gene, and therefore, may exhibit variable clinical signs that vary from near normal retina to severe disease and vision loss. The relationships between individual genetic mutations and disease severity in X-linked carriers requires further study. This review summarises the current literature surrounding the spectrum of disease seen in female carriers of choroideremia and X-linked retinitis pigmentosa. Various classification systems are contrasted to accurately grade retinal disease. Furthermore, genetic mechanisms at the early embryonic stage are explored to potentially explain the variability of disease seen in female carriers. Future research in this area will provide insight into the association between genotype and retinal phenotypes of female carriers, which will guide in the management of these patients. This review acknowledges the importance of identifying which patients may be at high risk of developing severe symptoms, and therefore should be considered for emerging treatments, such as retinal gene therapy.
... TPdh -/-T cells displayed an absence of Pdha ( Figure 1A). Similar to humans, Pdha is encoded on the X-chromosome 11 . Therefore, to determine the e cacy of our cre-recombinase and the utility of male and female mice for experiments, we studied both sexes for the presence of PDHA by immunoblot ( Figure 1B). ...
Background
Modulation of metabolic flux through pyruvate dehydrogenase complex (PDC) plays an important role in T cell activation and differentiation. PDC sits at the transition between glycolysis and the tricarboxylic acid cycle and is a major producer of acetyl-CoA, marking it as a potential metabolic and epigenetic node.
Methods
To understand the role of pyruvate dehydrogenase complex in T cell differentiation, we generated mice deficient in T cell pyruvate dehydrogenase E1A (Pdha) subunit using a CD4-cre recombinase-based strategy. To control for the contribution of exogenous metabolites in vivo, we conducted our T cell functional studies in vitro. T cells were differentiated into memory and effector T cells using standardized protocols. Cells were analyzed using stable isotopic tracing studies, metabolomics, RNAseq, ATACseq, ChIPseq and histone proteomics.
Results
Herein, we show that genetic ablation of PDC activity in T cells (TPdh-/-) leads to marked perturbations in glycolysis, the tricarboxylic acid cycle, and OXPHOS. Due to depressed OXPHOS, TPdh-/- T cells became dependent upon substrate level phosphorylation via glycolysis. Due to the block of PDC activity, histone acetylation was reduced, as were most other types of post translational modifications. Transcriptional and functional profiling revealed abnormal CD8⁺ memory T cell differentiation in vitro.
Conclusions
Collectively, our data indicate that PDC integrates the metabolome and epigenome in memory T cell differentiation. Targeting this metabolic and epigenetic node can have widespread ramifications on cellular function.
... the hypoxanthine phosphoribosyltransferase (Hprt) locus on the X chromosome (Samuel et al., 2016). In female mammals, dosage compensation of X-linked genes between males and females occurs by genetic inactivation of one of the two X chromosomes (Goto and Monk, 1998). The choice of X chromosome to be inactivated is random in female somatic cells. ...
The cardiomyocyte phenotypic switch from a proliferative to terminally differentiated state results in the loss of regenerative potential of the mammalian heart shortly after birth. Nonmuscle myosin IIB (NM IIB)-mediated actomyosin contractility regulates cardiomyocyte cytokinesis in the embryonic heart, and NM IIB levels decline after birth suggesting a role for cellular tension in the regulation of cardiomyocyte cell cycle activity in the postnatal heart. To investigate the role of actomyosin contractility in cardiomyocyte cell cycle arrest, we conditionally-activated ROCK2 kinase domain (ROCK2:ER) in the murine postnatal heart. Here we show that α5/β1 integrin and fibronectin matrix increase in response to actomyosin-mediated tension. Moreover, activation of ROCK2:ER promotes nuclear translocation of Yap, a mechanosensitive transcriptional co-activator, and enhances cardiomyocyte proliferation. Finally, we show that reduction of myocardial α5 integrin rescues the myocardial proliferation phenotype in ROCK2:ER hearts. These data demonstrate that cardiomyocytes respond to increase intracellular tension by altering their intercellular contacts in favor of cell-matrix interactions leading to Yap nuclear translocation, thus uncovering a novel function for nonmuscle myosin contractility in promoting cardiomyocyte proliferation in the postnatal heart.
... The consistent finding that ketone exposure is specifically detrimental to female offspring development, both in the present study and previously (Whatley et al., 2022), is particularly concerning, and the cause and longterm developmental consequences of this phenomenon should be explored further. Prior to X chromosome inactivation, occurring first in the TE lineage at the late blastocyst stage (Goto and Monk, 1998), female embryos have two active X chromosomes, encoding several metabolic genes including the glycolytic rate-limiting enzyme, glucose-6-phosphate dehydrogenase (Epstein et al., 1978;Gardner et al., 2010). Female preimplantation embryos are thus more glycolytic than males, observed both in the mouse (Gardner and Leese, 1987;Gardner et al., 2010;Lane and Gardner, 1996) and human (Gardner et al., 2011). ...
Research question
: Does the ketone acetoacetate (AcAc) alone, or combined with β-hydroxybutyrate (βOHB), impact mouse embryo development, metabolism, histone acetylation, and viability?
Design
: Pronucleate mouse oocytes were cultured in vitro in G1/G2 media supplemented with ketones (AcAc or AcAc + βOHB) at concentrations representing maternal serum levels during pregnancy (0.04 mM AcAc, 0.1 mM βOHB), standard diet consumption (0.1 mM AcAc, 0.25 mM βOHB), ketogenic diet consumption (0.8 mM AcAc, 2 mM βOHB), and diabetic ketoacidosis (2 mM AcAc, 4 mM βOHB). Day 5 blastocysts were assessed for cell allocation, glucose metabolism, and histone acetylation. Day 4 blastocysts exposed to 0.8 mM AcAc + 2 mM βOHB were transferred to standard-fed recipient females, and E14.5 fetal and placental development assessed.
Results
: Exposure to 2 mM AcAc or 0.8 mM AcAc + 2 mM βOHB did not impair blastocyst development, but significantly increased glucose consumption (P < 0.01), lowered glycolytic flux (P < 0.01), and elevated trophectoderm (TE) histone 3 lysine 27 acetylation (H3K27ac; P < 0.001) compared with unexposed controls. Preimplantation AcAc + βOHB exposure further reduced post-implantation fetal development by 25% (P < 0.05), and delayed female-specific fetal limb development (P < 0.05) and estimated fetal age (P < 0.05) compared with controls.
Conclusion
: Preimplantation exposure to ketones affects underlying metabolism and histone acetylation in blastocysts that are associated with persistent, female-specific perturbations in fetal development. A periconceptional diet that elevates ketone levels may impair human embryonic viability.
... X-chromosome upregulation in sheep has been supported by results from RNA sequencing (RNA seq) [4]. During male meiosis in some animal species, the X and Y become transcriptionally silenced in a process known as meiotic sex chromosome inactivation (MSCI) [10]. Following the initiation of MSCl, chromosomes undergo various genetic modification. ...
Dosage compensation is a mechanism first proposed by Susumu Ohno, whereby X inactivation balances X gene output between males (XY) and females (XX), while X upregulation balances X genes with autosomal gene output. These mechanisms have been actively studied in Drosophila and mice, but research regarding them lags behind in domestic species. It is unclear how the X chromosome is regulated in the sheep male germline. To address this, using single-cell RNA sequencing, we analyzed testes in three important developmental stages of sheep. We observed that the total RNA per cell from X and autosomes peaked in SSCs and spermatogonia and was then reduced in early spermatocytes. Furthermore, we counted the detected reads per gene in each cell type for X and autosomes. In cells experiencing dose compensation, close proximity to MSL (male-specific lethal), which is regulated the active X chromosome and was observed. Our results suggest that there is no dose compensation in the pre-meiotic germ cells of sheep testes and, in addition, MSL1 and MSL2 are expressed in early germ cells and involved in regulating mammalian X-chromosome inactivation and activation.
... In Figure 4, it can be observed that three samples with methylation consistency above 94% are derived from male, while samples with methylation consistency ranging from 54 to 72% are derived from female which is much lower than that of other homologous autosomes. It coincides with the previous studies that the methylation between two homologous chromosome X in female are different, one of which is inactive and highly methylated (Mohandas et al., 1981;Goto and Monk, 1998). ...
Different DNA methylation patterns presented on different tissues or cell types are considered as one of the main reasons accounting for the tissue-specific gene expressions. In recent years, many methods have been proposed to identify differentially methylated regions (DMRs) based on the mixture of methylation signals from homologous chromosomes. To investigate the possible influence of homologous chromosomes on methylation analysis, this paper proposed a method (MHap) to construct methylation haplotypes for homologous chromosomes in CpG dense regions. Through comparing the methylation consistency between homologous chromosomes in different cell types, it can be found that majority of paired methylation haplotypes derived from homologous chromosomes are consistent, while a lower methylation consistency was observed in the breast cancer sample. It also can be observed that the hypomethylation consistency of differentiated cells is higher than that of the corresponding undifferentiated stem cells. Furthermore, based on the methylation haplotypes constructed on homologous chromosomes, a method (MHap_DMR) is developed to identify DMRs between differentiated cells and the corresponding undifferentiated stem cells, or between the breast cancer sample and the normal breast sample. Through comparing the methylation haplotype modes of DMRs in two cell types, the DNA methylation changing directions of homologous chromosomes in cell differentiation and cancerization can be revealed. The code is available at: https://github.com/xqpeng/MHap_DMR.
... In addition to age, biological sex is another key variable that dictates DNA methylation patterns; in large part due to the fact that females display a DNA methylation dependent inactivation of the extra X-chromosome to regulate the dosage of X-linked gene in females (100). Several studies suggest that females secrete more insulin compared to males and are more insulin-sensitive (101,102). ...
Pancreatic beta cells play a central role in regulating glucose homeostasis by secreting the hormone insulin. Failure of beta cells due to reduced function and mass and the resulting insulin insufficiency can drive the dysregulation of glycemic control, causing diabetes. Epigenetic regulation by DNA methylation is central to shaping the gene expression patterns that define the fully functional beta cell phenotype and regulate beta cell growth. Establishment of stage-specific DNA methylation guides beta cell differentiation during fetal development, while faithful restoration of these signatures during DNA replication ensures the maintenance of beta cell identity and function in postnatal life. Lineage-specific transcription factor networks interact with methylated DNA at specific genomic regions to enhance the regulatory specificity and ensure the stability of gene expression patterns. Recent genome-wide DNA methylation profiling studies comparing islets from diabetic and non-diabetic human subjects demonstrate the perturbation of beta cell DNA methylation patterns, corresponding to the dysregulation of gene expression associated with mature beta cell state in diabetes. This article will discuss the molecular underpinnings of shaping the islet DNA methylation landscape, its mechanistic role in the specification and maintenance of the functional beta cell phenotype, and its dysregulation in diabetes. We will also review recent advances in utilizing beta cell specific DNA methylation patterns for the development of biomarkers for diabetes, and targeting DNA methylation to develop translational approaches for supplementing the functional beta cell mass deficit in diabetes.
... (v) hypoacetylation of histone H4; (vi) expression of the XIST (X inactive specific transcript) gene located at the X-inactivation center [9]. ...
Through the use of new genomic and metabolomic technologies, our comprehension of the molecular and biochemical etiologies of genetic disorders is rapidly expanding, and so are insights into their varying phenotypes. Dosage compensation (lyonization) is an epigenetic mechanism that balances the expression of genes on heteromorphic sex chromosomes. Many studies in the literature have suggested a profound influence of this phenomenon on the manifestation of X-linked disorders in females. In this review, we summarize the clinical and genetic findings in female heterozygotic carriers of a pathogenic variant in one of ten selected X-linked genes whose defects result in metabolic disorders.
... While promoter methylation is generally associated with transcriptional gene silencing, gene body hypermethylation correlates with gene activation [7]. Methylation is also essential for X-chromosome inactivation, development and differentiation [8]. Since DNA methylation modifies the potential function and physical properties of the base, changes in methylation could also influence genome integrity and cancer by altering various processes either directly through mutations involving base changes and coding outcomes or more broadly through the DDR and DNA repair. ...
Cells encounter a multitude of external and internal stress-causing agents that can ultimately lead to DNA damage, mutations and disease. A cascade of signaling events counters these challenges to DNA, which is termed as the DNA damage response (DDR). The DDR preserves genome integrity by engaging appropriate repair pathways, while also coordinating cell cycle and/or apoptotic responses. Although many of the protein components in the DDR are identified, how chemical modifications to DNA impact the DDR is poorly understood. This review focuses on our current understanding of DNA methylation in maintaining genome integrity in mammalian cells. DNA methylation is a reversible epigenetic mark, which has been implicated in DNA damage signaling, repair and replication. Sites of DNA methylation can trigger mutations, which are drivers of human diseases including cancer. Indeed, alterations in DNA methylation are associated with increased susceptibility to tumorigenesis but whether this occurs through effects on the DDR, transcriptional responses or both is not entirely clear. Here, we also highlight epigenetic drugs currently in use as therapeutics that target DNA methylation pathways and discuss their effects in the context of the DDR. Finally, we pose unanswered questions regarding the interplay between DNA methylation, transcription and the DDR, positing the potential coordinated efforts of these pathways in genome integrity. While the impact of DNA methylation on gene regulation is widely understood, how this modification contributes to genome instability and mutations, either directly or indirectly, and the potential therapeutic opportunities in targeting DNA methylation pathways in cancer remain active areas of investigation.
... 1. Atoms -the use of radioactive isotopes of atoms in enzyme substrates to isolate mutants in DNA synthesis to identify the genes involved, and the development of highly sensitive single cell molecular biology to measure specific enzyme activities in single cells (many references in the review by Goto & Monk, 1998, and for clinical relevance see . ...
... 2. Molecules -the study of genes, gene modifications and gene expression, involved in DNA replication and repair, gene expression in embryos, germ cells and cancers, regulation of gene expression in development, epigenetic modification directing gene activity, molecular mechanisms of Lamarckian inheritance (see many references in the review by Goto & Monk, 1998, and earlier references e.g., Monk & Kinross, 1972;Monk, 1990;Adjaye et al., 1997; and later references, e.g., Goto et al., 1999;Zuccotti & Monk, 1995). ...
