Methylation status of genes escaping from X-chromosome inactivation in patients with X-chromosome rearrangements

Abstract Background X-chromosome inactivation (XCI) is a mechanism in which one of two X chromosomes in females is randomly inactivated in order to compensate for imbalance of gene dosage between sexes. However, about 15% of genes on the inactivated X chromosome (Xi) escape from XCI. The methylation level of the promoter region of the escape gene is lower than that of the inactivated genes. Dxz4 and/or Firre have critical roles for forming the three-dimensional (3D) structure of Xi. In mice, disrupting the 3D structure of Xi by deleting both Dxz4 and Firre genes led to changing of the escape genes list. To estimate the impact for escape genes by X-chromosome rearrangements, including DXZ4 and FIRRE, we examined the methylation status of escape gene promoters in patients with various X-chromosome rearrangements. Results To detect the breakpoints, we first performed array-based comparative genomic hybridization and whole-genome sequencing in four patients with X-chromosome rearrangements. Subsequently, we conducted array-based methylation analysis and reduced representation bisulfite sequencing in the four patients with X-chromosome rearrangements and controls. Of genes reported as escape genes by gene expression analysis using human hybrid cells in a previous study, 32 genes showed hypomethylation of the promoter region in both male controls and female controls. Three patients with X-chromosome rearrangements had no escape genes with abnormal methylation of the promoter region. One of four patients with the most complicated rearrangements exhibited abnormal methylation in three escape genes. Furthermore, in the patient with the deletion of the FIRRE gene and the duplication of DXZ4, most escape genes remained hypomethylated. Conclusion X-chromosome rearrangements are unlikely to affect the methylation status of the promoter regions of escape genes, except for a specific case with highly complex rearrangements, including the deletion of the FIRRE gene and the duplication of DXZ4.

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Functional analysis of ectodysplasin-A mutations and involvement of X-chromosome inactivation

10.21203/rs.3.rs-602940/v1 ◽

2021 ◽

Author(s):

Yuhua Pan ◽

Ting Lu ◽

Ling Peng ◽

Qi Zeng ◽

Xiangyu Huang ◽

...

Keyword(s):

Functional Analysis ◽

X Chromosome ◽

Pcr Amplification ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Tooth Agenesis ◽

Human Dental Pulp ◽

Underlying Mechanisms ◽

The Impact ◽

Female Carriers

Abstract Objectives: The aim of this study was to identify genetic clues for the causes of familial non-syndromic oligodontia and explore the underlying mechanisms involved, while focusing on the role of human dental pulp stem cells (hDPSCs).Materials and Methods: Candidate gene sequences were obtained by PCR amplification and Sanger sequencing. Functional analysis was conducted, and the pathogenesis associated with EDA mutations in hDPSCs was investigated to explore the impact of the identified mutation on the phenotype. Capillary electrophoresis (CE) was used to detect X chromosome inactivation (XCI) in the blood of female carriers.Results: In this study, we identified an EDA mutation in a Chinese family：the missense mutation c.1013C>T (Thr338Met). Transfection of hDPSCs with a mutant EDA lentivirus decreased the expression of EDA and dentin sialophosphoprotein (DSPP) compared with transfection of control EDA lentivirus. Mechanistically, mutant EDA inhibited the activation of the NF-κB pathway. The CE results showed that symptomatic female carriers had a skewed XCI with a preferential inactivation of the X chromosome that carried the normal allele.Conclusions: In summary, we demonstrated that EDA mutations result in non-syndromic tooth agenesis in heterozygous females and that, mechanistically, EDA regulates odontogenesis through the NF-κB signalling pathway in hDPSCs.Clinical Relevance: Due to the large heterogeneity of tooth agenesis, this study provided a genetic basis for individuals who exhibit similar clinical phenotypes.

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X-linked clonality testing: interpretation and limitations

Blood ◽

10.1182/blood-2006-09-018655 ◽

2007 ◽

Vol 110 (5) ◽

pp. 1411-1419 ◽

Cited By ~ 45

Author(s):

George L. Chen ◽

Josef T. Prchal

Keyword(s):

X Chromosome ◽

Methylation Status ◽

X Chromosome Inactivation ◽

Protein Isoforms ◽

Chromosome Inactivation ◽

Detection Methods ◽

Parental Origin ◽

Genetic Changes ◽

Clonal Population ◽

Inactive X Chromosome

Abstract Clonality often defines the diseased state in hematology. Clonal cells are genetically homogenous and derived from the same precursor; their detection is based on genotype or phenotype. Genotypic clonality relies on somatic mutations to mark the clonal population. Phenotypic clonality identifies the clonal population by the expression pattern of surrogate genes that track the clonal process. The most commonly used phenotypic clonality methods are based on the X-chromosome inactivation principle. Clonality detection based on X-chromosome inactivation patterns (XCIP) requires discrimination of the active from the inactive X chromosome and differentiation of each X chromosome's parental origin. Detection methods are based on detection of X-chromosome sequence polymorphisms identified by protein isoforms, transcribed mRNA, and methylation status. Errors in interpreting clonality tests arise from stochastic, genetic, and cell selection pressures on the mechanism of X inactivation. Progressive X-chromosome skewing has recently been suggested by XCIP clonality studies in aging hematopoietic cells. This has led to new insights into the pathophysiology of X-linked and autoimmune disorders. Other research applications include combining XCIP clonality testing with genetic clonality testing to identify clonal populations with yet-to-be-discovered genetic changes.

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Role of G(-43)A polymorphism in the promoter region of the Xist gene in non-random x-chromosome inactivation in intraspecific hybrid voles

Russian Journal of Genetics ◽

10.1134/s1022795410100224 ◽

2010 ◽

Vol 46 (10) ◽

pp. 1233-1235

Author(s):

K. E. Orischenko ◽

E. A. Elisaphenko ◽

S. M. Zakian

Keyword(s):

X Chromosome ◽

Promoter Region ◽

X Chromosome Inactivation ◽

Xist Gene ◽

Chromosome Inactivation ◽

Intraspecific Hybrid

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The Impact of X-Chromosome Inactivation on Phenotypic Expression of X-Linked Neurodevelopmental Disorders

Brain Sciences ◽

10.3390/brainsci11070904 ◽

2021 ◽

Vol 11 (7) ◽

pp. 904

Author(s):

Boudewien A Brand ◽

Alyssa E Blesson ◽

Constance L. Smith-Hicks

Keyword(s):

X Chromosome ◽

Neurodevelopmental Disorders ◽

Phenotypic Expression ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Brain Functioning ◽

General Review ◽

Males And Females ◽

The Impact

Nearly 20% of genes located on the X chromosome are associated with neurodevelopmental disorders (NDD) due to their expression and role in brain functioning. Given their location, several of these genes are either subject to or can escape X-chromosome inactivation (XCI). The degree to which genes are subject to XCI can influence the NDD phenotype between males and females. We provide a general review of X-linked NDD genes in the context of XCI and detailed discussion of the sex-based differences related to MECP2 and FMR1, two common X-linked causes of NDD that are subject to XCI. Understanding the effects of XCI on phenotypic expression of NDD genes may guide the development of stratification biomarkers in X-linked disorders.

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Functional Analysis of Ectodysplasin-A Mutations in X-Linked Non-Syndromic Hypodontia and Possible Involvement of X-Chromosome Inactivation

10.21203/rs.3.rs-270895/v1 ◽

2021 ◽

Author(s):

Yuhua Pan ◽

Ting Lu ◽

Ling Peng ◽

Qi Zeng ◽

Xiangyu Huang ◽

...

Keyword(s):

Stem Cells ◽

Functional Analysis ◽

X Chromosome ◽

Dental Pulp ◽

X Chromosome Inactivation ◽

Dental Pulp Stem Cells ◽

Chromosome Inactivation ◽

Tooth Agenesis ◽

Human Dental Pulp ◽

The Impact

Abstract BackgroundMutations of the Ectodysplasin-A (EDA) gene are generally associated with other developmental anomalies (syndrome hypohidrotic ectodermal dysplasia) or as an isolated condition (non-syndromic tooth agenesis). The influence of EDA mutations on dentinogenesis and odontoblast differentiation have not been reported. The aim of the present study was to identify genetic clues for familial nonsyndromic oligodontia and explore the underlying mechanisms, focusing on the role of human dental pulp stem cells (hDPSCs).MethodsThe candidate genes sequences were performed by PCR amplification and Sanger sequencing. Functional analysis and pathogenesis associated with EDA mutations in hDPSCs were also investigated to explore the impact of the identified mutation on this phenotype. Capillary electrophoresis (CE) was used to detect X chromosome inactivation (XCI) on the blood of female carrier.ResultsIn this study, we identified a reported EDA mutation in a Chinese family：a missense mutation c.1013C>T (Thr338Met). Transfection of hDPSCs with mutant EDA lentivirus decreased the expression of EDA and dentin sialophosphoprotein (DSPP) compared with those transfected with control EDA lentivirus. Mechanically, the mutant EDA inhibited the activation of the NF-κB pathway. The results of CE showed that symptomatic female carrier had a skewed XCI with a preferential inactivation of the X chromosome carrying the normal allele.ConclusionIn summary, we demonstrated EDA mutation result in non-syndromic tooth agenesis in heterozygous females and mechanically EDA regulates odontogenesis through the NF-κB signaling pathway in human dental pulp stem cells.

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Functional Analysis of Ectodysplasin-A Mutations in X-Linked Nonsyndromic Hypodontia and Possible Involvement of X-Chromosome Inactivation

Stem Cells International ◽

10.1155/2021/7653013 ◽

2021 ◽

Vol 2021 ◽

pp. 1-10

Author(s):

Yuhua Pan ◽

Ting Lu ◽

Ling Peng ◽

Qi Zeng ◽

Xiangyu Huang ◽

...

Keyword(s):

Functional Analysis ◽

X Chromosome ◽

Pcr Amplification ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Chinese Family ◽

Tooth Agenesis ◽

Underlying Mechanisms ◽

The Impact ◽

Female Carriers

Background. Mutations of the Ectodysplasin-A (EDA) gene are generally associated with syndrome hypohidrotic ectodermal dysplasia or nonsyndromic tooth agenesis. The influence of EDA mutations on dentinogenesis and odontoblast differentiation has not been reported. The aim of this study was to identify genetic clues for the causes of familial nonsyndromic oligodontia and explore the underlying mechanisms involved, while focusing on the role of human dental pulp stem cells (hDPSCs). Materials and Methods. Candidate gene sequences were obtained by PCR amplification and Sanger sequencing. Functional analysis was conducted, and the pathogenesis associated with EDA mutations in hDPSCs was investigated to explore the impact of the identified mutation on the phenotype. Capillary electrophoresis (CE) was used to detect X-chromosome inactivation (XCI) in the blood of female carriers. Results. In this study, we identified an EDA mutation in a Chinese family: the missense mutation c.1013C>T (Thr338Met). Transfection of hDPSCs with a mutant EDA lentivirus decreased the expression of EDA and dentin sialophosphoprotein (DSPP) compared with transfection of control EDA lentivirus. Mechanistically, mutant EDA inhibited the activation of the NF-κB pathway. The CE results showed that symptomatic female carriers had a skewed XCI with a preferential inactivation of the X chromosome that carried the normal allele. Conclusions. In summary, we demonstrated that EDA mutations result in nonsyndromic tooth agenesis in heterozygous females and that, mechanistically, EDA regulates odontogenesis through the NF-κB signalling pathway in hDPSCs. Due to the large heterogeneity of tooth agenesis, this study provided a genetic basis for individuals who exhibit similar clinical phenotypes.

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X Chromosome Inactivation Pattern is not Associated With Interindividual Variations in Thyroid Volume: A Study of Euthyroid Danish Female Twins

Twin Research and Human Genetics ◽

10.1375/twin.12.5.502 ◽

2009 ◽

Vol 12 (5) ◽

pp. 502-506 ◽

Cited By ~ 2

Author(s):

Thomas Heiberg Brix ◽

Pia Skov Hansen ◽

Finn Noe Bennedbæk ◽

Steen Joop Bonnema ◽

Kirsten Ohm Kyvik ◽

...

Keyword(s):

X Chromosome ◽

Twin Pair ◽

Receptor Gene ◽

Thyroid Volume ◽

X Chromosome Inactivation ◽

Cag Repeat ◽

Chromosome Inactivation ◽

Pcr Analysis ◽

Autoimmune Thyroid ◽

The Impact

AbstractAhigher frequency of skewed X chromosome inactivation (XCI) is found in patients with autoimmune thyroid disease (AITD) than in controls. Although goitre is often present in AITD, a recent study failed to show an association between XCI and clinically overt nontoxic goitre. However, the etiology of overt goitre is complex, and the mechanisms influencing thyroid volume may involve fewer factors than the mechanisms underlying overt goitre. In order to examine the impact of XCI on thyroid volume in euthyroid females, we studied whether within cohort (n= 138) and within twin pair (n= 69) differences in XCI are correlated with differences in thyroid volume. XCI was determined by PCR analysis of a polymorphic CAG repeat in the first exon of the androgen receptor gene. Thyroid volume was determined by ultrasound. Neither in the within cohort nor in the within twin pair analysis could we demonstrate a statistically significant association between XCI and thyroid volume: Regression coefficient (β) = 0.023 (95% confidence interval, –0.062–0.108),p= 0.592 and β = 0.038 (–0.080–0.156),p= 0.521, respectively. Controlling for potential confounders such as zygosity, age, TSH, smoking habits and use of oral contraceptives did not change the findings. In conclusion, in a sample of euthyroid Danish female twins, we found no evidence of a relationship between XCI pattern and thyroid volume.

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Escape from X chromosome inactivation and female bias of autoimmune diseases

Molecular Medicine ◽

10.1186/s10020-020-00256-1 ◽

2020 ◽

Vol 26 (1) ◽

Author(s):

Mohammad Javad Mousavi ◽

Mahdi Mahmoudi ◽

Somayeh Ghotloo

Keyword(s):

Autoimmune Diseases ◽

X Chromosome ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

X Chromosomes ◽

Female Sex Hormones ◽

Female Bias ◽

The Impact ◽

The Given ◽

Dual Expression

AbstractGenerally, autoimmune diseases are more prevalent in females than males. Various predisposing factors, including female sex hormones, X chromosome genes, and the microbiome have been implicated in the female bias of autoimmune diseases. During embryogenesis, one of the X chromosomes in the females is transcriptionally inactivated, in a process called X chromosome inactivation (XCI). This equalizes the impact of two X chromosomes in the females. However, some genes escape from XCI, providing a basis for the dual expression dosage of the given gene in the females. In the present review, the contribution of the escape genes to the female bias of autoimmune diseases will be discussed.

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Functional analysis of Ectodysplasin-A mutations in X-linked non-syndromic hypodontia and possible involvement of X-chromosome inactivation

10.21203/rs.3.rs-602940/v2 ◽

2021 ◽

Author(s):

Yuhua Pan ◽

Ting Lu ◽

Ling Peng ◽

Qi Zeng ◽

Xiangyu Huang ◽

...

Keyword(s):

Functional Analysis ◽

X Chromosome ◽

Pcr Amplification ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Tooth Agenesis ◽

Human Dental Pulp ◽

Underlying Mechanisms ◽

The Impact ◽

Female Carriers

Abstract Background: Mutations of the Ectodysplasin-A (EDA) gene are generally associated with syndrome hypohidrotic ectodermal dysplasia or non-syndromic tooth agenesis. The influence of EDA mutations on dentinogenesis and odontoblast differentiation have not been reported. The aim of this study was to identify genetic clues for the causes of familial non-syndromic oligodontia and explore the underlying mechanisms involved, while focusing on the role of human dental pulp stem cells (hDPSCs). Materials and Methods: Candidate gene sequences were obtained by PCR amplification and Sanger sequencing. Functional analysis was conducted, and the pathogenesis associated with EDA mutations in hDPSCs was investigated to explore the impact of the identified mutation on the phenotype. Capillary electrophoresis (CE) was used to detect X chromosome inactivation (XCI) in the blood of female carriers. Results: In this study, we identified an EDA mutation in a Chinese family：the missense mutation c.1013C>T (Thr338Met). Transfection of hDPSCs with a mutant EDA lentivirus decreased the expression of EDA and dentin sialophosphoprotein (DSPP) compared with transfection of control EDA lentivirus. Mechanistically, mutant EDA inhibited the activation of the NF-κB pathway. The CE results showed that symptomatic female carriers had a skewed XCI with a preferential inactivation of the X chromosome that carried the normal allele. Conclusions: In summary, we demonstrated that EDA mutations result in non-syndromic tooth agenesis in heterozygous females and that, mechanistically, EDA regulates odontogenesis through the NF-κB signalling pathway in hDPSCs. Due to the large heterogeneity of tooth agenesis, this study provided a genetic basis for individuals who exhibit similar clinical phenotypes.

Download Full-text