scholarly journals Patchy, incomplete, and heterogeneous X-inactivation in the human placenta

2019 ◽  
Author(s):  
Tanya N. Phung ◽  
Kimberly C. Olney ◽  
Harvey J. Kliman ◽  
Melissa A. Wilson
Keyword(s):  
X Chromosome ◽  
Human Placenta ◽  
Strong Evidence ◽  
Prenatal Testing ◽  
Female Offspring ◽  
X Inactivation ◽  
Single Individual ◽  
X Chromosomes ◽  
Healthy Pregnancy ◽  
Single Region

AbstractThe placenta is formed after the first few weeks of pregnancy and is the genotype of the fetus. It acts as an immune modulator in the uterine environment to sustain a successful pregnancy. One of the X chromosomes in XX females is silenced by a process called X-inactivation. Prior research suggests that incorrect dosage on the X chromosome could lead to poor development of the placenta and ultimately result in complications in pregnancy. Previous studies of X- inactivation in the placenta were either in non-human placentas, or were limited to only a few SNPs and genes in human placentas. Thus, it is not clear whether within human placenta, X- inactivation is completely homogeneous, patchy, or mosaic. Further, X-inactivation is not complete in humans; as many as one-third of the genes on the X chromosome escape X- inactivation, but variability in genes that escape X-inactivation in the placenta has not been investigated. We sequenced RNA from 60 placenta samples from 30 full-term, uncomplicated pregnancies with female offspring. We can confidently rule out X-inactivation being completely mosaic in the human placenta. Rather, we find strong evidence that X-inactivation in the human placenta is patchy, with large potential clonal expansions of either silenced maternal or paternal X-chromosomes, with provocative suggestions of bias towards silencing the paternal X. We also find variation in the degree of silencing, where a high portion of variants (between 26.8-75.3% in any sample) are silenced incompletely. Finally, we find evidence for variability in genes that escape X-inactivation within and among placenta samples.SignificanceThe placenta is formed early during development, is essential for healthy pregnancy, and is largely composed of DNA from the offspring, and thus can be XX or XY. One of the X chromosomes in XX females is silenced by a process called X-inactivation. We studied patterns of X-inactivation in two regions of the placenta across 30 placentas, and find strong evidence for large patches of either maternally or paternally silenced X-chromosomes in the human placenta. We also found that the genes that escape X-inactivation vary both across individuals, and within the placenta of a single individual, suggesting mechanisms for variability in placenta function, and implications for prenatal testing that samples only a single region of the placenta.

scholarly journals Random X Inactivation and Extensive Mosaicism in Human Placenta Revealed by Analysis of Allele-Specific Gene Expression along the X Chromosome

PLoS ONE ◽  
2010 ◽  
Vol 5 (6) ◽  
pp. e10947 ◽  
Author(s):  
Joana Carvalho Moreira de Mello ◽  
Érica Sara Souza de Araújo ◽  
Raquel Stabellini ◽  
Ana Maria Fraga ◽  
Jorge Estefano Santana de Souza ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Human Placenta ◽  
X Inactivation ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Allele Specific

scholarly journals Human Genes Escaping X-inactivation Revealed by Single Cell Expression Data

2018 ◽  
Author(s):  
Kerem Wainer Katsir ◽  
Michal Linial
Keyword(s):  
Single Cell ◽  
X Chromosome ◽  
Noncoding Rna ◽  
Phenotypic Variability ◽  
Cell Types ◽  
X Inactivation ◽  
Specific Expression ◽  
X Chromosomes ◽  
Human Genes ◽  
Cumulative Knowledge

AbstractBackgroundIn mammals, sex chromosomes pose an inherent imbalance of gene expression between sexes. In each female somatic cell, random inactivation of one of the X-chromosomes restores this balance. While most genes from the inactivated X-chromosome are silenced, 15-25% are known to escape X-inactivation (termed escapees). The expression levels of these genes are attributed to sex-dependent phenotypic variability.ResultsWe used single-cell RNA-Seq to detect escapees in somatic cells. As only one X-chromosome is inactivated in each cell, the origin of expression from the active or inactive chromosome can be determined from the variation of sequenced RNAs. We analyzed primary, healthy fibroblasts (n=104), and clonal lymphoblasts with sequenced parental genomes (n=25) by measuring the degree of allelic-specific expression (ASE) from heterozygous sites. We identified 24 and 49 candidate escapees, at varying degree of confidence, from the fibroblast and lymphoblast transcriptomes, respectively. We critically test the validity of escapee annotations by comparing our findings with a large collection of independent studies. We find that most genes (66%) from the unified set were previously reported as escapees. Furthermore, out of the overlooked escapees, 11 are long noncoding RNA (lncRNAs).ConclusionsX-chromosome inactivation and escaping from it are robust, permanent phenomena that are best studies at a single-cell resolution. The cumulative information from individual cells increases the potential of identifying escapees. Moreover, despite the use of a limited number of cells, clonal cells (i.e., same X-chromosomes are coordinately inhibited) with genomic phasing are valuable for detecting escapees at high confidence. Generalizing the method to uncharacterized genomic loci resulted in lncRNAs escapees which account for 20% of the listed candidates. By confirming genes as escapees and propose others as candidates from two different cell types, we contribute to the cumulative knowledge and reliability of human escapees.

Regulation of imprinted X-chromosome inactivation in mice by Tsix

Development ◽  
2001 ◽  
Vol 128 (8) ◽  
pp. 1275-1286 ◽  
Author(s):  
T. Sado ◽  
Z. Wang ◽  
H. Sasaki ◽  
E. Li
Keyword(s):  
X Chromosome ◽  
X Chromosome Inactivation ◽  
X Inactivation ◽  
Chromosome Inactivation ◽  
Maternal Allele ◽  
Xist Expression ◽  
Developmental Defects ◽  
X Chromosomes ◽  
Embryonic Tissues ◽  
Early Embryonic Lethality

In mammals, X-chromosome inactivation is imprinted in the extra-embryonic lineages with paternal X chromosome being preferentially inactivated. In this study, we investigate the role of Tsix, the antisense transcript from the Xist locus, in regulation of Xist expression and X-inactivation. We show that Tsix is transcribed from two putative promoters and its transcripts are processed. Expression of Tsix is first detected in blastocysts and is imprinted with only the maternal allele transcribed. The imprinted expression of Tsix persists in the extra-embryonic tissues after implantation, but is erased in embryonic tissues. To investigate the function of Tsix in X-inactivation, we disrupted Tsix by insertion of an IRES(β)geo cassette in the second exon, which blocked transcripts from both promoters. While disruption of the paternal Tsix allele has no adverse effects on embryonic development, inheritance of a disrupted maternal allele results in ectopic Xist expression and early embryonic lethality, owing to inactivation of both X chromosomes in females and single X chromosome in males. Further, early developmental defects of female embryos with maternal transmission of Tsix mutation can be rescued by paternal inheritance of the Xist deletion. These results provide genetic evidence that Tsix plays a crucial role in maintaining Xist silencing in cis and in regulation of imprinted X-inactivation in the extra-embryonic tissues.

Molecular Characterization of Tiny Ring X Chromosomes from Females with Functional X Chromosome Disomy and Lack of cis X Inactivation

Genomics ◽  
1995 ◽  
Vol 27 (1) ◽  
pp. 182-188 ◽  
Author(s):  
Mihir M. Jani ◽  
Beth S. Torchia ◽  
G.Shashidhar Pai ◽  
Barbara R. Migeon
Keyword(s):  
Molecular Characterization ◽  
X Chromosome ◽  
X Inactivation ◽  
X Chromosomes

scholarly journals The search for the mouse X-chromosome inactivation centre

1990 ◽  
Vol 56 (2-3) ◽  
pp. 99-106 ◽  
Author(s):  
S. Rastan ◽  
S. D. M. Brown
Keyword(s):  
X Chromosome ◽  
Strong Evidence ◽  
Molecular Level ◽  
Molecular Genetic ◽  
X Chromosome Inactivation ◽  
X Inactivation ◽  
Chromosome Inactivation ◽  
Chromosome Identification ◽  
Female Embryo ◽  
Mary Lyon

SummaryThe phenomenon of X-chromosome inactivation in female mammals, whereby one of the two X chromosome present in each cell of the female embryo is inactivated early in development, was first described by Mary Lyon in 1961. Nearly 30 years later, the mechanism of X-chromosome inactivation remains unknown. Strong evidence has accumulated over the years, however, for the involvement of a major switch or inactivation centre on the mouse X chromosome. Identification of the inactivation centre at the molecular level would be an important step in understanding the mechanism of X-inactivation. In this paper we review the evidence for the existence and location of the X-inactivation centre on the mouse X-chromosome, present data on the molecular genetic mapping of this region, and describe ongoing strategies we are using to attempt to identify the inactivation centre at the molecular level.

Sex-ratio meiotic drive in Drosophila simulans: cellular mechanism, candidate genes and evolution

2006 ◽  
Vol 34 (4) ◽  
pp. 562-565 ◽  
Author(s):  
C. Montchamp-Moreau
Keyword(s):  
Sex Ratio ◽  
X Chromosome ◽  
Natural Populations ◽  
Meiotic Drive ◽  
Female Offspring ◽  
Drosophila Simulans ◽  
X Chromosomes ◽  
Individual Fitness ◽  
Primary Sex Ratio ◽  
Intragenomic Conflict

The sex-ratio trait, reported in a dozen Drosophila species, is a type of naturally occurring meiotic drive in which the driving elements are located on the X chromosome. Typically, as the result of a shortage of Y-bearing spermatozoa, males carrying a sex-ratio X chromosome produce a large excess of female offspring. The presence of sex-ratio chromosomes in a species can have considerable evolutionary consequences, because they can affect individual fitness and trigger extended intragenomic conflict. Here, I present the main results of the study performed in Drosophila simulans. In this species, the loss of Y-bearing spermatozoa is related to the inability of the Y chromosome sister-chromatids to separate properly during meiosis II. Fine genetic mapping has shown that the primary sex-ratio locus on the X chromosome contains two distorter elements acting synergistically, both of which are required for drive expression. One element has been genetically mapped to a tandem duplication. To infer the natural history of the trait, the pattern of DNA sequence polymorphism in the surrounding chromosomal region is being analysed in natural populations of D. simulans harbouring sex-ratio X chromosomes. Initial results have revealed the recent spread of a distorter allele.

scholarly journals Studies on Metatherian Sex Chromosomes III. The Use of Tritiated Uridine-induced Chromosome Aberrations to Distinguish Active and Inactive X Chromosomes

1977 ◽  
Vol 30 (2) ◽  
pp. 103 ◽  
Author(s):  
Jennifer A Donald ◽  
DW Cooper
Keyword(s):  
X Chromosome ◽  
Sex Chromosomes ◽  
Chromosome Aberrations ◽  
X Inactivation ◽  
Facultative Heterochromatin ◽  
Hybrid Female ◽  
X Chromosomes ◽  
Toxicity Effect ◽  
Red Kangaroo ◽  
Chromosome Regions

The paternal X inactivation system of kangaroos has been investigated in this study by using tritiated uridine-induced chromosome aberrations to distinguish the active from the inactive X. Previous work in eutherian mammals has demonstrated that constitutive heterochromatic chromosome regions are less susceptible to breakage by tritiated uri dine than euchromatic regions. The results of a comparison between the paternal X chromosome of a wallaroo x red kangaroo hybrid female and the two X chromosomes of a red kangaroo female suggested that the facultative heterochromatin of the X is also less susceptible to breakage by this treatment. However there were significantly more breaks of the paternal X in fibroblasts than in lymphocytes of the hybrid female, which agrees with biochemical findings suggesting activation of the paternal X in fibroblasts. Our results strengthen the suggestion of other workers that the reduced number of aberrations in heterochromatin occurs because such breaks occur principally when the DNA and labelled RNA are in apposition during transcription. Some evidence was found of an apparent toxicity effect of the tritiated uridine solution on the cells.

scholarly journals Functional Analysis of the DXPas34Locus, a 3′ Regulator of Xist Expression

1999 ◽  
Vol 19 (12) ◽  
pp. 8513-8525 ◽  
Author(s):  
E. Debrand ◽  
C. Chureau ◽  
D. Arnaud ◽  
P. Avner ◽  
E. Heard
Keyword(s):  
X Chromosome ◽  
Yeast Artificial Chromosome ◽  
Es Cells ◽  
Artificial Chromosome ◽  
Antisense Transcription ◽  
Regulatory Elements ◽  
X Inactivation ◽  
X Chromosomes ◽  
Inactivation Center ◽  
Controlling Element

ABSTRACT X inactivation in female mammals is controlled by a key locus on the X chromosome, the X-inactivation center (Xic). The Xic controls the initiation and propagation of inactivation in cis. It also ensures that the correct number of X chromosomes undergo inactivation (counting) and determines which X chromosome becomes inactivated (choice). The Xist gene maps to the Xic region and is essential for the initiation of X inactivation in cis. Regulatory elements of X inactivation have been proposed to lie 3′ toXist. One such element, lying 15 kb downstream ofXist, is the DXPas34 locus, which was first identified as a result of its hypermethylation on the active X chromosome and the correlation of its methylation level with allelism at the X-controlling element (Xce), a locus known to affect choice. In this study, we have tested the potential function of theDXPas34 locus in Xist regulation and X-inactivation initiation by deleting it in the context of largeXist-containing yeast artificial chromosome transgenes. Deletion of DXPas34 eliminates both Xistexpression and antisense transcription present in this region in undifferentiated ES cells. It also leads to nonrandom inactivation of the deleted transgene upon differentiation. DXPas34 thus appears to be a critical regulator of Xist activity and X inactivation. The expression pattern of DXPas34 during early embryonic development, which we report here, further suggests that it could be implicated in the regulation of imprintedXist expression.

Genetic activity of sex chromosomes in somatic cells of mammals

1970 ◽  
Vol 259 (828) ◽  
pp. 41-52 ◽  
Keyword(s):  
X Chromosome ◽  
Germ Cells ◽  
Chromosome Region ◽  
Somatic Cells ◽  
X Inactivation ◽  
X Chromosomes ◽  
Animal Group ◽  
Inactive X Chromosome ◽  
Genetic Activity ◽  
Partial Inactivation

Mammals are thought to have a type of dosage compensation not so far known in any other animal group: however many X chromosomes are present, only one remains genetically active in somatic cells. Considerable evidence for this idea exists, in spite of criticism; the greatest difficulty is presented by the abnormalities in human individuals with X chromosome aberrations. Possible explanations for these abnormalities include: wrong X chromosome dosage in early development before X inactivation, reversal of inactivation, partial inactivation of both X chromosomes, activity of the X while in the condensed inactive state, and the presence of a homologous non-inactivated region of the human X and Y. In female germ cells X inactivation apparently does not occur, but the situation in male germ cells is less clear. The Y chromosome is probably also inactive in somatic cells of adults, but again its function in germ cells is not yet clear. Some species have a presumed doubly inactive X chromosome region, as well as the singly active one. The origins and functions of this region are unknown; it may have a role in female germ cells.

scholarly journals A RIF1 and KAP1-based, double-bookmarking system generates a toggle switch that stabilises the identities of the active and inactive X chromosomes during random X inactivation in mouse

2020 ◽  
Author(s):  
Elin Enervald ◽  
Rossana Foti ◽  
Lynn Marie Powell ◽  
Agnieszka Piszczek ◽  
Sara C.B. Buonomo
Keyword(s):  
X Chromosome ◽  
Embryonic Stem ◽  
X Inactivation ◽  
Allelic Association ◽  
Toggle Switch ◽  
X Chromosomes ◽  
Non Coding Rna ◽  
The Future ◽  
Long Non Coding Rna ◽  
Stochastic Event

ABSTRACTDosage compensation for the X chromosome-linked genes in female placental mammals is achieved through the random silencing of one of the two X chromosomes. The onset of random X inactivation in mouse embryos and in differentiating embryonic stem cells requires the switch from a symmetric state, where both X chromosomes are equivalent, to an asymmetric state, where the identity of the future inactive and active X chromosomes are assigned. This “choice”, initiated by a stochastic event, needs to evolve into a stable and transmissible state. The transition from bi- to mono-allelic expression of the long non-coding RNA Tsix is thought to be one of the initial events breaking the symmetry of the two X chromosomes. Here we show that the asymmetric expression of Tsix triggers in turn the switch of RIF1 association with the Xist promoter from dynamic and symmetric to stable and asymmetric (on the future inactive X). On the future inactive X, RIF1 then plays an essential role in the upregulation of Xist, thus initiating the consolidation and stable transmission of the identity of the inactive X. Tsix-dependent exclusion of RIF1 from the future active X chromosome in turn permits the association of KAP1 with the Xist promoter, thus marking the future active X chromosome. Timely mono-allelic association of KAP1 is important for a stable choice and for X inactivation. We present here a double-bookmarking system, based on the mutually exclusive relationships of Tsix and RIF1, and RIF1 and KAP1. This system coordinates the identification of the active and inactive X chromosomes and initiates a self-sustaining loop that transforms an initially stochastic event into a stably inherited asymmetric X chromosome state.

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